These actions led MacArthur to be viewed as the new Imperial force in Japan by many Japanese political and civilian figures, even being considered to be the rebirth of the Shogun style government[2] which Japan was ruled under until the start of the Meiji Restoration Period.

As soon as November 26, 1945, MacArthur confirmed to admiral Mitsumasa Yonai that the emperor's abdication would not be necessary.[4] Before the war crimes trials actually convened, SCAP, the IPS and Shōwa officials worked behind the scenes not only to prevent the imperial family being indicted, but also to slant the testimony of the defendants to ensure that no one implicated the Emperor. High officials in court circles and the Shōwa government collaborated with Allied GHQ in compiling lists of prospective war criminals, while the individuals arrested as Class A suspects and incarcerated in Sugamo Prison solemnly vowed to protect their sovereign against any possible taint of war responsibility.[5]

As Supreme Commander for the Allied Powers, MacArthur also gave immunity to Shiro Ishii and all members of the bacteriological research units in exchange for germ warfare data based on human experimentation. On May 6, 1947, he wrote to Washington that "additional data, possibly some statements from Ishii probably can be obtained by informing Japanese involved that information will be retained in intelligence channels and will not be employed as "War Crimes" evidence."[6] The deal was concluded in 1948.[7]

According to popular historian Herbert Bix in Hirohito and the Making of Modern Japan, "MacArthur's truly extraordinary measures to save the Emperor from trial as a war criminal had a lasting and profoundly distorting impact on Japanese understanding of the lost war."[8]

Toward the end of the occupation, Emperor Hirohito let it be known to SCAP that he was prepared to apologize formally to U.S. Gen. MacArthur for Japan's actions during World War II – including an apology for the December 7, 1941 attack on Pearl Harbor.[9]

Patrick Lennox Tierney had an intimate perspective on events which unfolded in SCAP headquarters. Tierney's office was on the fifth floor of the Dai-Ichi Insurance Building in Tokyo, the same floor where MacArthur's suite of offices was located. He was there on the day the Emperor came to offer this apology; but when the emperor arrived, MacArthur refused to admit him or acknowledge him. A pivotal moment passed. Many years later, Tierney made an effort to explain his understanding of the significance of what he had personally witnessed: "Apology is a very important thing in Japan."[9] Issues which might have been addressed were allowed to remain open, and consequences unfolded across the decades which followed.[10]

Above the political and economic control SCAP had for the seven years following Japan’s surrender, SCAP also had strict control over all of the Japanese media, under the formation of the Civil Censorship Detachment (CCD) of SCAP. The CCD eventually banned a total of 31 topics from all forms of media.[2] These topics included: