President George W. Bush ordered Jose Padilla, detained by the US Military as an alleged terrorist, to be transferred out of military custody in order to face trial in a federal criminal court. He is charged with conspiracy to commit murder, kidnapping, aiding terrorist groups and other acts against US nationals outside the United States. These actions come six days ahead of a decision by the US Supreme Court on whether it should review the 4th U.S. Circuit Court of Appeal's ruling that the president is authorised to hold Padilla as an "Enemy Combatant" without charge. 
Jose Padilla, a US citizen born in Brooklyn, has been held without charge in a military brig at a US Navy detention facility in South Carolina for the three-and-a-half years since his arrest in 2002. The administration had at the time alleged that Padilla was plotting to detonate a Radioactive "dirty" bomb in the US and later, Deputy Attorney General James Comey alleged that he was involved in plots to blow up Hotels and high-rise buildings[1]. The present indictment does not include any charges over these allegations. Instead, Padilla is charged with travelling abroad to train in "violent Jihad", providing material support to terrorists by sending money, physical assets, and new recruits to Jihadi groups, and conspiring to murder individuals overseas[2]. 
The change in custody restores to Padilla a number of rights he had been denied when the administration designated him as an "Enemy Combatant", including the right to access federal courts and be defended by an attorney. That constitutionality of detaining suspects without charge under this designation has been challenged in court, on behalf of Padilla and in September, a 3-judge panel of the 4th US Circuit Court of Appeals upheld the government's powers to detain Padilla. The Supreme Court was set to decide on whether it will review that decision next week. Padilla's status, for the purpose of this trial, is that of an ordinary criminal indictee, possessing the legal rights conferred on him by the US Bill of Rights.
The existence of the classification of "enemy combatant" has no precedent in either US or international law, and allows detention without reference to the customary judicial protections for criminal defendants in the US, and also without reference to the acts of congress and the agreements made in the Geneva Conventions regarding the treatment of prisoners of war.
Several precedents exist for the habeas petition  put forth by Padilla's attorney, Donna Newman. In June 2004, the Supreme Court ruled in the case of Yaser Hamdi that enemy combatants captured on foreign battlefields were entitled to some due process determination of their status. Hamdi was released on condition that he remain in his parent's homeland Saudi Arabia. Hamdi is a US citizen who had been captured among Taliban fighters in Afghanistan and who was similarly classified as an enemy combatant. In a case decided around the same time, the high court ruled that  prisoners at Guantánamo could seek habeas relief in US courts. It, however, avoided ruling on Padilla’s petition and voted 5-4 that Padilla's initial appeal should have been  in Charleston, South Carolina, where he was being held, rather than in New York, where he was first held as a material witness.
Padilla’s attorney, Donna Newman, filed a new habeas petition in South Carolina, where United States District Judge Henry F. Floyd ruled that Padilla was required to be charged with a crime or released. Floyd wrote of the Bush administration’s position that “were ever adopted by the courts, it would totally eviscerate the limits placed on presidential authority to protect the citizenry’s individual liberties”. Floyd is one of the justices appointed by President Bush. Floyd’s decision was reversed in September of 2005 by a three-judge panel of the Fourth Circuit Court of Appeals, led by Michael J. Luttig. Luttig claimed that Padilla served as a guard for the Taliban and Al Qaeda in Afghanistan during the period that US troops were engaged in combat against those organizations, and that he then “traveled to the United States for the avowed purpose of further prosecuting that war on American soil, against American citizens and targets”.
Padilla filed a second petition last month with the Supreme Court that was aimed at appealing Luttig’s ruling. Padilla’s lawyers intend to continue to proceed in the Supreme Court after the release of their client from military custody. Andrew Patel, Newman’s co-counsel, said on the radio show Democracy Now! that “the threat posed by the Bush administration’s invocation of the "enemy combatant" doctrine still exists". Patel further stated in opposition to the claim by Gonzales claim during the Tuesday indictment announcement that the case is moot, "We will ask the Court to consider this very important issue. Not only is it not moot as to Mr. Padilla—for example, suppose he was acquitted of this charge or the case was somehow dismissed, and the government decided that, 'Well, we don’t want him out,' and they just declare him to be an enemy combatant and send him back to the brig again. Until the Supreme Court rules that the president does not have that power, that's an authority, as Justice Jackson said in his dissent to Korematsu [the World War II Japanese-American internment case], that lies around like a loaded gun ready to be used or abused at any time."
The development of this case began with Padilla's arrest at Chicago’s O’Hare Airport in May of 2002. Former Attorney General John Ashcroft announced in June of the same year that a plot to explode a radioactive dirty bomb in America had been stopped; and described as a goal of several Al Qaeda operatives, including Padilla. On this basis, President Bush declared Padilla to be an “enemy combatant,” and authorized his transfer to a Naval brig, with the requisite limitations on his developing of a defense thus imposed by the classification. By June 2004, court reverses allowed Padilla to meet with legal council. Additional charges of plotting to destroy hotels and apartment buildings were claimed against Padilla by the Justice Department. These charges, however, were not included in the indictment released Tuesday.
This indictment focused on conspiracy charges against Padilla, particularly that he conspired with Adham Amin Hassoun, Kifah Wael Jayyousi, Mohammed Hesham Youssef and Kassem Daher to send funds, physical assets and recruits intended to continue fighting in Afghanistan, Algeria, Bosnia, Chechnya, Lebanon, Libya and Somalia. Further, it is charged that this was done through multiple front groups, including the American Islamic Group, the Islamic Center of the Americas, and Save Bosnia Now. The support for this conspiracy is claimed to have begun in 1993 and continue until November 2001 and consists of conversations obtained by wiretaps including alleged code words including "friends,” “football,” “tourism,” “fresh air,” and “picnics,”. The indictment further includes various payments of ranges from 1,000 to 5,000 USD. Padilla is mentioned as a "recruit" who had traveled to Egypt and Afghanistan where he completed a “Mujahideen Data Form”. He is not alleged to have engaged in any violent activities. 
Gonzales also alleged that the conspiracy advocated "acts of physical violence such as murder, maiming, kidnapping and hostage-taking against innocent civilians," but this was not included in the Tuesday indictment.
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Bush backtracks over legal status of alleged "Dirty Bomber" Jose Padilla