An American man who disappeared in Iran more than six years ago had been working for the CIA in what U.S. intelligence officials describe as a rogue operation that led to a major shake-up in the spy agency. 
 
 Robert Levinson, a retired FBI agent, traveled to the Iranian island of Kish in March 2007 to investigate corruption at a time when he was discussing the renewal of a CIA contract he had held for several years. He also inquired about getting re­imbursed for the Iran trip by the agency before he departed, according to former and current U.S. intelligence officials. 
 
 After he vanished, CIA officials told Congress in closed hearings as well as the FBI that Levinson did not have a current relationship with the agency and played down its ties with him. Agency officials said Levinson did not go to Iran for the CIA. 
 
 But months after Levinson’s abduction, e-mails and other documents surfaced that suggested he had gone to Iran at the direction of certain CIA analysts who had no authority to run operations overseas. That revelation prompted a major internal investigation that had wide-ranging repercussions, the officials said, speaking on the condition of anonymity. 
 
 The CIA leadership disciplined 10 employees, including three veteran analysts who were forced out of their jobs, the officials said. 
 
 This undated handout photo was provided by the family of Robert Levinson. They received it in April of 2011. (Uncredited/AP) 
 
 The agency changed the rules outlining how analysts conduct business with contractors, including academics and other subject-matter experts who don’t work at the CIA, making it harder for agency employees to have such relationships. 
 
 The CIA ultimately concluded that it was responsible for Levinson while he was in Iran and paid $2.5 million to his wife, Christine, former U.S. intelligence officials said. The agency also paid the family an additional $120,000, the cost of renewing Levinson’s contract. 
 
 Levinson’s whereabouts remain unknown. Investigators can’t even say for certain whether he’s still alive. The last proof of life came about three years ago when the Levinson family received a video of him and later pictures of him shackled and dressed in an orange jumpsuit similar to those worn by detainees at the prison at Guantanamo Bay, Cuba. 
 
 “I have been held here for 31 / 2 years,” he says in the video. “I am not in good health.” 
 
 U.S. intelligence officials concede that if he is alive, Levinson, who would be 65, probably would have told his captors about his work for the CIA, as he was likely subjected to harsh interrogation. 
 
 The National Security Council declined to comment on any ties Levinson has to the U.S. government. “The investigation into Mr. Levinson’s disappearance continues, and we all remain committed to finding him and bringing him home safely to his family,” said spokeswoman Caitlin Hayden. 
 
 In a statement released Thursday, Levinson’s family said the U.S. government has failed to make saving his life a priority. “It is time for the U.S. government to step up and take care of one of its own. After nearly 7 years, our family should not be struggling to get through each day without this wonderful, caring, man that we love so much,” the statement said. 
 
 Levinson joined the FBI’s New York Field Office in 1978 after spending six years with the Drug Enforcement Administration. He was an expert on the New York mob’s five families. Eventually, he moved to the Miami office, where he tracked Russian organized-crime figures and developed a reputation for developing sources. 
 
 While in the FBI, Levinson attended a conference where he met a well-respected CIA analyst named Anne Jablonski, one of the agency’s experts on Russia. The two formed a friendship. 
 
 When Levinson retired from the FBI in 1998, he went to work as a private investigator. 
 
 Jablonski continued at the agency and, among her other duties after the Sept. 11, 2001, attacks on the United States, was to brief FBI Director Robert S. Mueller and Attorney General John D. Ashcroft. By 2005, she was in the Office of Transnational Issues (OTI), the CIA unit that tracks money transfers, weapons smuggling and organized crime. 
 
 Jablonski brought Levinson to the CIA for discussions on money laundering with her colleagues. In 2006, Tim Sampson, then the head of the Illicit Finance Group, which was part of OTI, hired Levinson. The unclassified contract was then worth $85,000. 
 
 Academic reports 
 
 Levinson was supposed to provide academic reports but was operating more like a spy, gathering intelligence for the CIA and producing numerous well- 
 
 received reports, officials said. While working for the CIA, he passed on details about the Colombian rebels, then-President Hugo Chávez of Venezuela and Iran’s nuclear program. 
 
 Levinson hopscotched the globe. He went to Turkey and Canada, among other countries, to interview potential sources, sometimes using a fake name. But CIA station chiefs in those countries were never notified of Levinson’s activities overseas even though the agency reimbursed him for his travel, a violation of the rules. 
 
 On March 8, 2007, Levinson flew from Dubai to the Iranian island of Kish and checked into a hotel. He met with Dawud Salahuddin, a fugitive wanted for the murder of an Iranian dissident and diplomat who was shot at his house in Bethesda, Md. Levinson thought Salahuddin could supply details about the Iranian regime, perhaps ones that could interest the CIA, according to officials who have reconstructed some of his movements. 
 
 Levinson spent hours talking to Salahuddin. The next morning, he checked out of his hotel and vanished, officials said. The United States suspected the Iranian security services were behind his abduction, according to a diplomatic cable disclosed by WikiLeaks. 
 
 The U.S. government insisted that Levinson was a private citizen making a private trip. The State Department, in a cable to U.S. embassies in May 2007, said much the same thing. “Levinson was not working for the United States government,” Secretary of State Condoleezza Rice wrote. 
 
 The CIA told the Senate Intelligence Committee that Levinson had done some minor work for the agency but that his contract had run out and the spy agency had nothing to do with him going to Iran. Agency analysts also spoke with the FBI and said they hadn’t sent him to Iran. The CIA’s involvement seemed to end there. The FBI, which investigates crimes against Americans, did not push the CIA to open its files and take a deeper look at Levinson’s relationship with the agency. 
 
 But Levinson’s family and friends refused to accept that he was a lost tourist. A former federal prosecutor in Florida named David McGee, a friend of Levinson’s, and McGee’s paralegal, Sonya Dobbs, thought the government wasn’t being truthful about who employed Levinson. 
 
 Dobbs managed to access Levinson’s e-mail accounts. There she found e-mails between Jablonski and Levinson and other material suggesting that he had worked with the CIA in what appeared to be a continuing relationship. 
 
 One of the e-mails instructed Levinson not to worry about getting paid for going to Iran shortly before he made the trip. Jablonski said she would take care of it. She advised him not to contact the agency’s contract office. “Keep talk about the additional money among us girls,” she said by e-mail. 
 
 The e-mails also suggested that Levinson was operating at Ja­blonski’s behest, according to officials who have reviewed the communications between the two. Jablonski adamantly denied in an interview that she oversaw what Levinson was doing. 
 
 With the newly discovered information, McGee got the attention of Sen. Bill Nelson (D-Fla.), who serves on the intelligence panel and is from Levinson’s home state. At the CIA, agency investigators began to scrutinize Levinson’s relationship with Jablonski and her boss, Sampson, and discovered more problems in the handling of his work. 
 
 Instead of mailing reports to the CIA, where they would be properly screened and processed, Jablonski had Levinson send them to her house, according to officials. She said she could review them faster that way. 
 
 They used private e-mail accounts to communicate — one reason the CIA was slow to learn of the relationship. The arrangement led CIA investigators to think Jablonski was trying to obscure their ties, according to current and former U.S. officials. 
 
 Jablonski never disclosed those details and others to investigators when Levinson disappeared. While the FBI and CIA knew about Levinson’s previous contract, answers she provided “didn’t square with the e-mails,” said a former senior agency official with knowledge of the events. 
 
 To CIA officials, it appeared that she was running a source and collecting intelligence, a job for trained operatives in the clandestine service and not analysts. In fact, the CIA’s clandestine arm never knew that Levinson was on the payroll or his activities when he traveled abroad, officials said. 
 
 By 2008, the CIA’s deputy director at the time, Stephen Kappes, conceded to Nelson and other senators that there was more to the Levinson story than the agency had acknowledged the previous year. Some on the committee said they had been misled by the CIA. 
 
 Jablonski said in an interview that she wasn’t hiding anything from CIA officials and that they knew about the arrangement with Levinson. Jablonksi said she would never put Levinson, a friend, in harm’s way. 
 
 Nevertheless, Jablonski and Sampson could face criminal charges, law enforcement officials say. Both veteran analysts resigned from the CIA in 2008 along with a third senior manager. Jablonski now works in the private sector. Sampson took a job with the Department of Homeland Security. He declined to comment for this report. 
 
 He told the Associated Press: “I didn’t even know he was working on Iran. As far as I knew he was a Latin America, money-laundering and Russian-organized-crime guy. I would never have directed him to do that.” 
 
 A break in 2010 
 
 For years, Levinson’s family had no word on the fate of the former FBI agent. A break came in November 2010 when an unknown source sent the family a 54-second video of Levinson, who appeared haggard but otherwise unharmed. They are unsure who sent the video, or why. The FBI is also unsure when the video was made. 
 
 “Please help me get home,” he says in the video. “Thirty-three years of service to the United States deserves something. Please help me.” 
 
 Levinson spent only 28 years with the Drug Enforcement Administration and the FBI, suggesting that he was including his time on a CIA contract as part of his government service. 
 
 A few months later, the family received a series of pictures: Levinson, his hands chained and his hair long and unruly, dressed in an orange jumpsuit. The family received them in April 2011. The FBI determined that they were sent from Afghanistan but was unsure when they were taken. 
 
 The photographs and videos turned into a dead end. And a recent FBI media blitz and $1 million reward haven’t revealed his whereabouts. Secret FBI meetings with the Iranians in Europe also have proved fruitless, officials said. 
 
 After the video and pictures of Levinson emerged, American officials concocted a story that he was being held in Pakistan or Afghanistan in an effort to provide the Iranians some cover to release him, according to U.S. intelligence officials. Then-Secretary of State Hillary Rodham Clinton put out a statement in March 2011 that Levinson might be in southwest Asia. Officials hoped Levinson would turn up in one of those two countries and give the Iranians plausible deniability, officials said. 
 
 The ruse failed. 
 
 U.S. intelligence officials say that if there was a moment for his return, it was when they received the video. They can’t explain why Iran has freed other captives, such as a trio of U.S. hikers, but not Levinson. And other U.S. citizens being held by Iran — pastor Saeed Abedini and former Marine Amir Hekmati — are known to be alive, unlike Levinson. 
 
 The Iranians have steadfastly denied holding Levinson. Even as the relationship between the United States and Iran has thawed with the recent election of President Hassan Rouhani and a temporary deal that freezes parts of the country’s nuclear program, there has been no progress on securing Levinson or information about his fate. 
 
 “We don’t know where he is, who he is,” Rouhani told CNN in September during the United Nations General Assembly. “He is an American who has disappeared. We have no news of him.” 
 
 U.S. intelligence officials remain skeptical. They suspect Iran did snatch Levinson, but they can’t prove it. Officials surmise that only a professional intelligence service such as Iran’s Ministry of Intelligence and National Security could have taken Levinson and thwarted American efforts to find him for so many years. 
 
 U.S. intelligence officials acknowledge it’s very possible Levinson, who was in poor health, died under questioning at some point. They say there is no upside for the Iranians to admit he died in their custody. 
 
 Former officials familiar with the case said releasing the information about his CIA ties won’t make his situation any worse. 
 
 Levinson’s family refuses to believe he is dead and remains hopeful he will return home. 
 
 In November, Levinson became the longest-held hostage in U.S. history, surpassing the 2,454 days that Terry Anderson spent in captivity in Lebanon in the 1970s. 
 
 “No one would have predicted this terrible moment more than 61 / 2 years ago when Bob disappeared,” Christine Levinson said in a statement last month. “Our family will soon gather for our seventh Thanksgiving without Bob, and the pain will be almost impossible to bear. Yet, as we endure this terrible nightmare from which we cannot wake, we know that we must bear it for Bob, the most extraordinary man we have ever known.” 
 
 This article was reported beginning in 2010 while Goldman worked at the Associated Press. Goldman, whose byline also appears on an AP story on this subject, is now a Post staff writer. 

 This undated handout photo provided by the family of Robert Levinson, shows retired-FBI agent Robert Levinson in a photo the family received in April 2011. In March 2007, Levinson flew to Kish Island,... (Associated Press) 
 
 In March 2007, retired FBI agent Robert Levinson flew to Kish Island, an Iranian resort awash with tourists, smugglers and organized crime figures. Days later, after an arranged meeting with an admitted killer, he checked out of his hotel, slipped into a taxi and vanished. For years, the U.S. has publicly described him as a private citizen who traveled to the tiny Persian Gulf island on private business. 
 
 But that was just a cover story. An Associated Press investigation reveals that Levinson was working for the CIA. In an extraordinary breach of the most basic CIA rules, a team of analysts _ with no authority to run spy operations _ paid Levinson to gather intelligence from some of the world's darkest corners. He vanished while investigating the Iranian government for the U.S. 
 
 The CIA was slow to respond to Levinson's disappearance and spent the first several months denying any involvement. When Congress eventually discovered what happened, one of the biggest scandals in recent CIA history erupted. 
 
 Behind closed doors, three veteran analysts were forced out of the agency and seven others were disciplined. The CIA paid Levinson's family $2.5 million to pre-empt a revealing lawsuit, and the agency rewrote its rules restricting how analysts can work with outsiders. 
 
 But even after the White House, FBI and State Department officials learned of Levinson's CIA ties, the official story remained unchanged. 
 
 "He's a private citizen involved in private business in Iran," the State Department said in 2007, shortly after Levinson's disappearance. 
 
 "Robert Levinson went missing during a business trip to Kish Island, Iran," the White House said last month. 
 
 Details of the unusual disappearance were described in documents obtained or reviewed by the AP, plus interviews over several years with dozens of current and former U.S. and foreign officials close to the search for Levinson. Nearly all spoke on condition of anonymity because they were not authorized to discuss the sensitive case. 
 
 The AP first confirmed Levinson's CIA ties in 2010 and continued reporting to uncover more details. It agreed three times to delay publishing the story because the U.S. government said it was pursuing promising leads to get him home. 
 
 The AP is reporting the story now because, nearly seven years after his disappearance, those efforts have repeatedly come up empty. The government has not received any sign of life in nearly three years. Top U.S. officials, meanwhile, say his captors almost certainly already know about his CIA association. 
 
 There has been no hint of Levinson's whereabouts since his family received proof-of-life photos and a video in late 2010 and early 2011. That prompted a hopeful burst of diplomacy between the United States and Iran, but as time dragged on, promising leads dried up and the trail went cold. 
 
 Some in the U.S. government believe he is dead. But in the absence of evidence either way, the government holds out hope that he is alive and the FBI says it remains committed to bringing him home. 
 
 If Levinson remains alive at age 65, he has been held captive longer than any American, longer than AP journalist Terry Anderson, who was held more than six years in Beirut. Unlike Anderson, Levinson's whereabouts and captors remain a mystery. 
 
 Today, Iran and United States tiptoe toward warmer relations and a deal over Iran's nuclear enrichment. But the U.S. has no new leads about Levinson's whereabouts, officials said. Iranian President Hassan Rouhani publicly says he has no information about Levinson's whereabouts. 
 
 Meanwhile, the story of how the married father of seven children became part of the CIA's spy war with Iran has been cloaked in secrecy, with no public accounting for the agency's mistakes. 
 
 ___ 
 
 A 28-year veteran of the Drug Enforcement Administration and the FBI, Robert Levinson had a natural ability to cultivate informants. Former colleagues say he was an easy conversationalist who had the patience to draw out people and win their confidence. He'd talk to anyone. 
 
 "Bob, in that sense, was fearless," said retired FBI Assistant Director Mark Mershon, who worked with Levinson in Miami in the 1980s. "He wasn't concerned about being turned down or turned away." 
 
 As the Soviet Union collapsed, Levinson turned his attention away from Mafia bosses and cocaine cartels and began watching the Russian gangsters who made their homes in Florida. Russian organized crime was a niche then and Levinson made a name as one of the few investigators who understood it. 
 
 At a Justice Department organized crime conference in Santa Fe, N.M., in the early 1990s, Levinson listened to a presentation by a CIA analyst named Anne Jablonski and spotted a kindred spirit. 
 
 Jablonski was perhaps the government's foremost expert on Russian organized crime. Former colleagues say she had an encyclopedic memory and could, at the mere mention of a crime figure, quickly explain his place in the hierarchy and his method of moving money. When White House officials had questions about Russian organized crime, they often called Jablonski directly. 
 
 In the relatively staid world of CIA analysts, Jablonski was also a quirky character, a yoga devotee who made her own cat food, a woman who skipped off to Las Vegas to renew her vows in an Elvis-themed chapel. 
 
 After the Santa Fe conference, Levinson left a note for Jablonski at her hotel and the two began exchanging thoughts on organized crime. Jablonski invited Levinson to CIA headquarters in Langley, Va., to speak to her colleagues in the Office of Russian and European Analysis. 
 
 By the time Levinson retired from the FBI in 1998, he and Jablonski were close friends. She attended his going-away party in Florida, met his family and harvested his knowledge of organized crime. 
 
 In retirement, Levinson worked as a private investigator, traveling the world and gathering information for corporate clients. Jablonski, meanwhile, thrived at the CIA. After the Sept. 11 attacks, former colleagues say, she was assigned to brief Attorney General John Ashcroft and FBI Director Robert Mueller about terrorist threats every morning. 
 
 In 2005, Jablonski moved to the Office of Transnational Issues, the CIA team that tracks threats across borders. Right away, she arranged for Levinson to speak to the money-laundering experts in the office's Illicit Finance Group. 
 
 In a sixth-floor CIA conference room, Levinson explained how to track dirty money. Unlike the analysts in the audience, Levinson came from the field. He generated his own information. 
 
 In June 2006, the head of Illicit Finance, Tim Sampson, hired Levinson on a contract with the CIA, former officials said. Like most CIA contracts, it was not a matter of public record. But it also wasn't classified. 
 
 ___ 
 
 At its core, the CIA is made up of two groups: operatives and analysts. Operatives collect intelligence and recruit spies. Analysts receive strands of information and weave them together, making sense of the world for Washington decision-makers. 
 
 Their responsibilities don't overlap. Operatives manage spies. Analysts don't. 
 
 Levinson was hired to work for a team of analysts. His contract, worth about $85,000, called for him to write reports for the CIA based on his travel and his expertise. 
 
 From the onset, however, he was doing something very different. He wasn't writing scholarly dissertations on the intricacies of money laundering. He was gathering intelligence, officials say. 
 
 He uncovered sensitive information about Colombian rebels. He dug up dirt on Venezuela's mercurial president. He delivered photos and documents on militant groups. And he met with sources about Iran's nuclear program, according to people who have reviewed the materials. 
 
 Levinson's production got noticed. The CIA expected he'd provide one or two items a month from his travels. Some months, former officials said, Levinson would send 20 packages including photos, computer disks and documents _ the work of a man with decades of investigative experience. 
 
 Levinson's arrangement with the CIA was odd. 
 
 The agency instructed him not to mail his packages to headquarters or email documents to government addresses, former officials said. Instead, he was told to ship his packages to Jablonski's home in Virginia. If he needed to follow up, he was instructed to contact Jablonski's personal email account. 
 
 Jablonski said the analysts simply wanted to avoid the CIA's lengthy mail screening process. As an employee, Jablonski could just drive the documents through the front gate each morning. 
 
 "I didn't think twice about it," she said in an interview. 
 
 But the normal way to speed up the process is to open a post office box or send packages by FedEx, officials say. And if Levinson were producing only unclassified analytical documents, there would have been no reason he couldn't email them to the CIA. 
 
 The whole arrangement was so peculiar that CIA investigators conducting an internal probe would later conclude it was an effort to keep top CIA officials from figuring out that the analysts were running a spying operation. Jablonski adamantly denies that. 
 
 What's more, the Illicit Finance Group didn't follow the typical routine for international travel. Before someone travels abroad for the agency, the top CIA officer in the country normally clears it. That way, if a CIA employee is arrested or creates a diplomatic incident, the agency isn't caught by surprise. 
 
 That didn't happen before Levinson's trips, former officials said. He journeyed to Panama, Turkey and Canada and was paid upon his return, people familiar with his travels said. After each trip, he submitted bills and the CIA paid him for the information and reimbursed him for his travel expenses. 
 
 Neither the analysts nor the contract officers or managers who reviewed the contract, ever flagged it as a problem that Levinson's travel might become a problem. 
 
 It would prove to be a serious problem. 
 
 Levinson was assigned a contract officer inside the agency, a young analyst named Brian O'Toole. But Jablonski was always his primary contact. Sometimes, he told her before he left for a trip. Other times, he didn't. The emails between Jablonski and Levinson, some of which the AP has seen or obtained, are circumspect. But they show that Levinson was taking his cues from her. 
 
 The more Levinson did for the agency, the more the analysts ran afoul of the CIA's most basic rules. 
 
 Before anyone can meet sources, seasoned CIA intelligence officials must review the plan to make sure the source isn't a double agent. That never happened for Levinson. 
 
 Levinson's meetings blurred the lines between his work as a private investigator and his work as a government contractor. Inside the CIA, the analysts reasoned that as long as they didn't specifically assign Levinson to meet someone, they were abiding by the rules. 
 
 On Feb. 5, 2007, Levinson emailed Jablonski and said he was gathering intelligence on Iranian corruption. He said he was developing an informant with access to the government and could arrange a meeting in Dubai or on an island nearby. 
 
 Problem was, Levinson's contract was out of money and, though the CIA was working to authorize more, it had yet to do so. 
 
 "I would like to know if I do, in fact, expend my own funds to conduct this meeting, there will be reimbursement sometime in the near future, or, if I should discontinue this, as well as any and all similar projects until renewal time in May," Levinson wrote. 
 
 There's no evidence that Jablonski ever responded to that email. And she says she has no recollection of ever receiving it. 
 
 A few days later, Levinson joined Jablonski and her husband for dinner at Harry's Tap Room in the Washington suburbs. Levinson was days away from his trip, and though he was eager to get paid for it, Jablonski says the subject never came up in conversation. 
 
 The discussion was more light-hearted, she said. She recalls scolding her overweight friend for not eating right, especially while on the road. At one point she recalls chiding him: "If I were your wife, I'd confiscate your passport." 
 
 On Feb. 12, Levinson again emailed Jablonski, saying he hadn't heard anything from the contract office. Jablonski urged him not to get the contract team involved. 
 
 "Probably best if we keep talk about the additional money among us girls _ you, me, Tim and Brian _ and not get the contracts folks involved until they've been officially notified through channels," Jablonski said, according to emails read to the AP. 
 
 Jablonski signed off: "Be safe." 
 
 Levinson said he understood. He said he'd try to make this trip as successful as previous ones. And he promised to "keep a low profile." 
 
 "I'll call you upon my return from across the pond," he said. 
 
 While Levinson was overseas, the CIA was raving about information Levinson had recent sent about Venezuela and Colombian rebels. 
 
 "You hit a home run out of the park with that stuff," she wrote. "We can't, of course, task you on anything, but let's just say it's GREAT material." 
 
 Levinson arrived in Dubai on March 3, 2007. Friends and investigators say he was investigating cigarette smuggling and also looking into Russian organized crime there. 
 
 On March 8, he boarded a short flight to Kish Island, a tourist destination about 11 miles off Iran's southern coast. Unlike the Dubai trip, this one was solely for the CIA. He was there to meet his source about Iran. 
 
 The biggest prize would be gleaning something about Iran's nuclear program, one of the CIA's most important targets. 
 
 Levinson's source on Kish was Dawud Salahuddin, an American fugitive wanted for killing a former Iranian diplomat in Maryland in 1980. In interviews with ABC News and the New Yorker, Salahuddin has admitted killing the diplomat 
 
 Since fleeing to Iran, Salahuddin had become close to some in the Iranian government, particularly to those seen as reformers and moderates. 
 
 To set up the meeting, Levinson worked with a longtime friend, retired NBC investigative reporter Ira Silverman. Silverman had talked at length with Salahuddin and, in a 2002 piece for the New Yorker magazine, portrayed him as a potential intelligence source if the U.S. could coax him out of Iran. The subtitle of the article: "He's an assassin who fled the country. Could he help Washington now?" 
 
 "I told them to put off until after the U.S. surge in Iraq was completed," Salahuddin told the National Security News Service, a Washington news site, shortly after Levinson disappeared. "But Silverman and Levinson pushed for the meeting and that's why we met in March." 
 
 Silverman's role in helping set up Levinson's meeting with Salahuddin has been previously disclosed. Silverman declined to discuss Levinson's disappearance. 
 
 Levinson's flight landed late the morning of March 8, a breezy, cloudy day. He checked into the Hotel Maryam, a few blocks off Kish's eastern beaches. Salahuddin has said he met with Levinson for hours in his hotel room. 
 
 The hotel's registry, which Levinson's wife has seen, showed him checking out on March 9, 2007. 
 
 ___ 
 
 Jablonski was in the office when news broke that Levinson had gone missing. She went to the bathroom and threw up. 
 
 FBI agents began asking about Levinson's disappearance and the CIA started a formal inquiry into whether anyone at the agency had sent Levinson to Iran or whether he was working for the CIA at the time. 
 
 The response from the analytical division was that, yes, Levinson had given a few presentations and had done some analytical work. But his contract was out of money. The agency had no current relationship with Levinson and there was no connection to Iran. 
 
 That's what the CIA told the FBI and Congress, according to numerous current and former FBI, CIA and congressional officials. 
 
 Jablonski never mentioned to internal investigators the many emails she'd traded with Levinson, officials close to the investigation said. When asked, she said she had no idea he was heading to Iran. She didn't tell managers or that Levinson expected to be reimbursed for the trip he was on, or that he was investigating Iranian corruption. 
 
 Jablonski says none of this was a secret; Levinson's contract and work product were available to others at the CIA, she said. 
 
 Because the emails were exchanged from her personal account, they were not available to investigators searching the CIA's computers. But had anyone at the CIA or FBI conducted even a cursory examination of Levinson's work product, it would have been immediately clear that Levinson was not acting as a mere analyst. 
 
 Had anyone read his invoices, people who have seen or been briefed on them said, investigators would have seen handwritten bills mentioning Iran and its Revolutionary Guard. 
 
 That didn't happen. 
 
 So the official story became that Levinson was in Iran on private business, either to investigate cigarette smuggling or to work on a book about Russian organized crime, which has a presence on Kish. 
 
 At the State Department, officials told the world that Levinson was a private businessman. 
 
 "At the time of his disappearance Mr. Levinson was not working for the United States government," the State Department said in a May 2007 message sent to embassies worldwide and signed by Secretary of State Condoleezza Rice. 
 
 Levinson's family feared the government had forsaken him. 
 
 The government's version would have remained the official story if not for Levinson's friends. One of them was David McGee, a former Justice Department prosecutor in Florida who had worked with Levinson when he was at the FBI. McGee, now in private practice at the Florida law firm Beggs and Lane, knew that Levinson was working for the CIA. He just couldn't prove it. 
 
 As time dragged on, McGee kept digging. Finally, he and his paralegal, Sonya Dobbs, discovered Levinson's emails with Jablonski. 
 
 They were astounded. And they finally had the proof they needed to get the government's attention. 
 
 Armed with the emails, McGee wrote to the Senate Intelligence Committee in October 2007. The CIA had indeed been involved in Levinson's trip, the letter proved. 
 
 The CIA had been caught telling Congress a story that was flatly untrue. The Intelligence Committee was furious. In particular, Levinson's senator, Bill Nelson, D-Fla., took a personal interest in the case. The committee controls the budget of the CIA, and one angry senator there can mean months of headaches for the agency. 
 
 CIA managers said their own employees had lied to them. They blamed the analysts for not coming forward sooner. But the evidence had been hiding in plain sight. The CIA didn't conduct a thorough investigation until the Senate got involved. By then, Levinson had been missing for more than eight months. Precious time had been lost. 
 
 Sampson said he was never aware of Levinson's emails with Jablonski or the Iranian trip. 
 
 "I didn't even know he was working on Iran," he said. "As far as I knew he was a Latin America, money-laundering and Russian organized crime guy. I would never have directed him to do that." 
 
 Finally, the CIA assigned its internal security team to investigate. That inquiry quickly determined that the agency was responsible for Levinson while he was in Iran, according to a former official familiar with the review. That was an important conclusion. It meant that, whatever happened to Levinson overseas, the CIA bore responsibility. 
 
 Next, a team of counterintelligence officers began unraveling the case. 
 
 The investigation renewed some longtime tensions between the CIA's operatives and analysts. The investigators felt the analysts had been running their own amateur spy operation, with disastrous results. Worse, they said the analysts withheld what they knew, allowing senior managers to testify falsely on Capitol Hill. 
 
 That led the Justice Department to investigate possible criminal charges against Jablonski and Sampson. Charges were never pursued, current and former officials said, in part because a criminal case could have revealed the whole story behind Levinson's disappearance. Officially, though, the investigation remains open. 
 
 Sampson offered to take a polygraph. Jablonski says she has consistently told the truth. Recently, as the five-year statute of limitations concluded, FBI agents interviewed her again and she told the same story, officials said. 
 
 The analysts argued that many people had seen Levinson's contract and his work product. Nobody questioned it until he went missing, they said. The way the analysts saw it, the CIA was looking for scapegoats. 
 
 "That she would even by accident put someone in harm's way is laughable," said Margaret Henoch, a former CIA officer and a close friend of Jablonski. "When I worked with Anne, and I worked very closely with her for a very long time, she was always the one who pulled me up short and made me follow procedure." 
 
 Jablonski said the CIA's relationship with Levinson was not unusual. But as part of the investigation, the CIA reviewed every analytical contract it had. 
 
 Only Levinson was meeting with sources, collecting information, and getting reimbursed for his trips, officials said. Only Levinson was mailing packages of raw information to the home of an analyst. 
 
 Despite Jablonski's denials, her emails convinced investigators that she knew Levinson was heading overseas and, with a wink and a nod, made it clear he could expect to be paid. 
 
 In May 2008, Jablonski was escorted from the building and put on administrative leave. Sampson was next. At the CIA, when you're shown the door, you leave with nothing. Security officers empty your desk, scrutinize its contents and mail you whatever doesn't belong to the agency. 
 
 Both were given the option of resigning or being fired. The next month, they resigned. Their boss was forced into retirement. At least seven others were disciplined, including employees of the contracts office that should have noticed that Levinson's invoices didn't square with his contract. 
 
 In secret Senate hearings from late 2007 through early 2008, CIA Deputy Director Stephen Kappes acknowledged that the agency had been involved in Levinson's disappearance and conceded that it hadn't been as forthcoming as it should have been, current and former officials said. 
 
 The CIA's top lawyer, John Rizzo, had to explain it all to the White House. Former Bush administration officials recall Rizzo meeting with a stunned Fred Fielding, the White House counsel who asked, since when do CIA analysts get involved in operations? 
 
 One of Rizzo's assistants, Joseph Sweeney, a lawyer, flew to Florida to apologize to Levinson's family. 
 
 The CIA paid the family about $120,000, the value of the new contract the CIA was preparing for him when he left for Iran. The government also gave the family a $2.5 million annuity, which provides tax-free income, multiple people briefed on the deal said. Neither side wanted a lawsuit that would air the secret details in public. 
 
 Jablonski now analyzes risk for companies doing business overseas. 
 
 Sampson, the former head of CIA's Illicit Finance group, quickly returned to the government, landing a job at the Department of Homeland Security's intelligence division. O'Toole, the young contracts officer, moved to the Treasury Department. He would not comment. 
 
 Inside the CIA, the biggest legacy of the Levinson case might be the strict new rules in place for analysts. Before, analysts were encouraged to build relationships with experts. An analyst could go to dinner with a professor of Middle East affairs or pick up the phone and chat with a foreign affairs expert. The 9/11 Commission encouraged CIA analysts to do even more to solicit outside views. 
 
 After the Levinson inquiry, the CIA handed down orders requiring analysts to seek approval for nearly any conversation with outsiders. The rules were intended to prevent another debacle like Levinson's, but former officials say they also chilled efforts to bring outside views into the CIA. 
 
 ___ 
 
 The U.S. always suspected, but could never prove, that Levinson had been picked up by Iranian security forces. What was not immediately clear, however, was whether Iran knew that Levinson was working for the CIA. 
 
 Now, nearly than seven years later, investigators believe Iranian authorities must know. Levinson wasn't trained to resist interrogation. U.S. officials could not imagine him withholding information from Iranian interrogators, who have been accused of the worst types of mental and physical abuses. 
 
 In an October 2010 interview with the AP, Mahmoud Ahmadinejad, the president of Iran at the time, said his country was willing to help find Levinson. But he appeared to suggest he knew or had suspicions that Levinson was working for the U.S. government. 
 
 "Of course if it becomes clear what his goal was, or if he was indeed on a mission, then perhaps specific assistance can be given," Ahmadinejad said. "For example, if he had plans to visit with a group or an individual or go to another country, he would be easier to trace in that instance." 
 
 As a CIA contractor, Levinson would have been a valuable chip to bargain with on the world stage. So if Iran had captured him, and knew his CIA ties, why the secrecy? 
 
 That question became even more confusing in 2009, when three U.S. hikers strayed across border from Iraq into Iran and were arrested. If Iran had captured Levinson, investigators wondered, why would it publicly accuse three hikers of espionage while keeping quiet about an actual CIA contractor? 
 
 Occasionally, Iranian defectors would claim to have seen Levinson or to have heard where he was being held, according to his family, former officials and State Department cables published by WikiLeaks. 
 
 A French doctor said Levinson was treated at his hospital in Tehran. An Iranian nurse claimed to have attended to him. One defector said he saw Levinson's name scrawled into a prison door frame. Someone sent Levinson's family what appeared to be secret Iranian court documents with his name on them. 
 
 But the U.S. could never confirm any of these accounts or corroborate the documents. 
 
 Occasionally, the family would hear from someone claiming to be the captor. Once, someone sent an email not only to the family, but also to other addresses that might have been stored on Levinson's phone. But despite efforts to try to start negotiating, the sender went silent. 
 
 The State Department continued its calls on Iran to release information about Levinson's whereabouts. Then, in November 2010, Levinson's wife Christine received an email from an unknown address. A file was attached, but it would not open. 
 
 Frantic, she sent the email to some computer savvy friends, who opened the file and held the phone to the computer. Christine Levinson immediately recognized her husband's voice. 
 
 "My beautiful, my loving, my loyal wife, Christine," he began. 
 
 The 54-second video showed Levinson sitting in front of a concrete wall, looking haggard but unharmed. He said he was running dangerously low of diabetes medicine, and he pleaded with the government to bring him home. 
 
 "Thirty-three years of service to the United States deserves something," Levinson said. "Please help me." 
 
 The video was a startling proof of life and it ignited the first promising round of diplomacy since Levinson's disappearance. U.S. officials met privately with members of the Iranian government to discuss the case. The Iranians still denied any knowledge of Levinson's whereabouts but said they were willing to help, U.S. officials said. 
 
 Some details about the video didn't add up, though. The email had been sent from a cyber cafe in Pakistan, officials said, and Pashtun wedding music played faintly in the background. The Pashtun people live primarily in Pakistan and Afghanistan, just across Iran's eastern border. 
 
 Further, the video was accompanied by a demand that the U.S. release prisoners. But officials said the United States was not holding anyone matching the names on the list. 
 
 In March 2011, after months of trying to negotiate with shadows, Secretary of State Hillary Clinton released a statement saying the U.S. had evidence that Levinson was being held "somewhere in southwest Asia." The implication was that Levinson might be in the hands of terrorist group or criminal organization somewhere in Pakistan or Afghanistan, not necessarily in Iran. 
 
 U.S. intelligence officials working the case still believed Iran was behind Levinson's disappearance, but they hoped Clinton's statement would offer a plausible alternative story if Iran wanted to release him without acknowledging it ever held him. 
 
 U.S. negotiators didn't care what the story was, as long as it ended with Levinson coming home. 
 
 The following month, the family received another email, this time from a new address, one that tracked back to Afghanistan. Photos were attached. Levinson looked far worse. His hair and beard were long and white. He wore an orange Guantanamo Bay-style jumpsuit. A chain around his neck held a sign in front of his face. Each picture bore a different message. 
 
 "Why you can not help me," was one. 
 
 Though the photos were disturbing, the U.S. government and Levinson's family saw them as a hopeful sign that whoever was holding Levinson was interested in making a deal. Then, a surprising thing happened. 
 
 Nothing. 
 
 Nobody is sure why the contact stopped. Some believe that, if Iran held him, all the government wanted was for the United States to tell the world that Levinson might not be in Iran after all. Others believe Levinson died. 
 
 Iran executes hundreds of prisoners each year, human rights groups say. Many others disappear and are presumed dead. With Levinson's history of diabetes and high blood pressure, it was also possible he died under questioning. 
 
 The discussions with Iran ended. A task force of CIA, FBI and State Department officials studied the case anew. Analysts considered alternative theories. Maybe Levinson was captured by Russian organized crime figures, smugglers or terrorists? They investigated connections between Russian and Iranian oil interests. 
 
 But each time, they came back to Iran. 
 
 For example, during one meeting between the U.S. and Iran, the Iranians said they were searching for Levinson and were conducting raids in Baluchistan, a mountainous region that includes parts of Pakistan, Iran and Afghanistan, U.S. officials said. But the U.S. ultimately concluded that there were no raids, and officials determined that the episode was a ruse by the Iranians to learn how U.S. intelligence agencies work. 
 
 Then, U.S. operatives in Afghanistan traced the hostage photos to a cellphone used to transmit them, officials said. They even tracked down the owner, but concluded he had nothing to do with sending them. 
 
 Such abrupt dead ends were indicative of a professional intelligence operation, the U.S. concluded. Whoever sent the photos and videos had made no mistakes. Mobsters and terrorists are seldom so careful. 
 
 Iran denies any knowledge of Levinson's whereabouts and says it's doing all it can. 
 
 This past June, Iran elected Hassan Rouhani as president. He has struck a more moderate tone than his predecessor, sparking hope for warmer relations between Iran and the West. But Rouhani's statements on Levinson were consistent with Ahmadinejad's. 
 
 "He is an American who has disappeared," Rouhani told CNN in September. "We have no news of him. We do not know where he is." 
 
 ___ 
 
 Back home in Florida, Christine Levinson works to keep her husband's name in the news and pushes the Obama administration to do more. Last year, the FBI offered a reward of $1 million for information leading to the return of her husband. But the money hasn't worked. 
 
 In their big, tight-knit family, Bob Levinson has missed many birthdays, weddings, anniversaries and grandchildren. 
 
 Levinson was always the breadwinner, the politically savvy investigator who understood national security. Now it is his wife who has traveled to Iran seeking information on her husband, who has meetings on Capitol Hill or with White House officials. They are kind and reassuring. 
 
 But nothing changes. 
 
 Others held in Iran have returned home. Not her husband. 
 
 "There isn't any pressure on Iran to resolve this," she said in January, frustrated with what she said was a lack of attention by Washington. "It's been much too long." 
 
 ___ 
 
 Follow Apuzzo at http://twitter.com/mattapuzzo
– Robert Levinson of Florida went missing in Iran in 2007, and the Washington Post and the AP are out with stories today that might better explain why: He was working as a sort of rogue operator for the CIA at the time. Or more precisely, the retired FBI agent was working for a small team of CIA analysts who apparently didn't fill in their superiors about what they were doing, which amounted to running unauthorized spy operations overseas, according to the two stories. The AP calls it "an extraordinary breach of the most basic CIA rules." After his disappearance, CIA officials said flatly that Levinson wasn't working for the agency, but Levinson's family uncovered emails between him and a CIA analyst named Anne Jablonksi, with whom he was friends. In one sent before his Iran trip, he asked about getting paid, and she told him to deal with her, not the CIA's contract office. “Keep talk about the additional money among us girls," she wrote. Jablonski has since left the agency and could face criminal charges, says the Post. As for Levinson, now 65, the last proof that he was alive came nearly three years ago. The best guess is that Iran is either holding him or knows where he is. The AP says it has held the story three times in recent years, but is publishing now because efforts to free Levinson have gone nowhere. It adds that his CIA affiliation is surely old news to his captors.