On April 4 Attorney General Eric Holder announced that Khalid Sheikh Mohammed, the alleged mastermind of the 9/11 attacks, would be tried along with four other Guantánamo Bay detainees before a military commission to be convened at the prison. The move has been depicted in the press as a capitulation to fierce congressional resistance to the administration’s efforts to dismantle the counterterrorism apparatus constructed by George W. Bush. Indeed, last December Congress passed legislation barring the transfer of Guantánamo prisoners to the United States, thereby blocking Obama’s attempt to try the prisoners in New York. In passing this legislation Congress denied Obama an option—to try before a federal court al Qaeda suspects held at Guantánamo—that Bush possessed though never exercised. Yet long before Congress took this stance, Obama endorsed many of the Bush policies governing prisoners at Guantánamo, including the use of military commissions. Although Congress frustrated the specific plans Obama had in mind for the trial of Khalid Sheikh Mohammed, he created the options that he then confronted, and thus must accept responsibility for the constitutional breaches they represent.

Soon after taking office, Obama signed executive orders banning torture and closing Guantánamo in one year’s time. The question remained what to do with some 250 detainees still at the prison. In a speech at the National Archives in May 2009, he announced a two-track policy for the trial of some Guantánamo prisoners: one group would be tried before civilian courts and the other before military commissions. He indicated no basis for making this allocation.

Following the speech Obama proposed legislation to revise the evidentiary rules governing military commissions. The result was the Military Commissions Act of 2009, under which Khalid Sheikh Mohammed and the other four Guantánamo prisoners will now be tried. In proposing this measure, Obama built upon similar initiatives by Bush, who had issued in November 2001 an executive order establishing military commissions for the trial of Guantánamo prisoners. In June 2006 the Supreme Court set aside Bush’s order, but it based its ruling on a conflict with a statute, not on a violation of the constitutional guarantee of due process, and Congress, acting at Bush’s urging, cured that defect by passing the Military Commissions Act of 2006. Obama, then a senator, voted against the 2006 Act.

Although the 2009 Act improved the rules of evidence established under Bush’s November 2001 executive order and the 2006 Act, the new procedures still fall short of the protections afforded the accused in a civilian trial. More important, the basic structural defect of the earlier measures—trial by military officers—remains. The 2009 Act thus constitutes a further institutionalization of an irregular alternative that the government might use—for reasons we will never wholly know—to prosecute suspected terrorists whom the president determines are not protected by the Third Geneva Convention (Bush referred to them as unlawful enemy combatants; Obama calls them unprivileged enemy belligerents). Like the earlier measures, the 2009 Act only applies to foreign nationals. This limitation on the jurisdiction of military commissions not only raises equal protection issues, but also testifies powerfully to the second-class character of the justice that commissions are likely to render: it is not good enough for Americans.

In the past, military commissions have been used on the battlefield to try belligerents caught red-handed and accused of war crimes. In such circumstances they have been allowed as tribunals of necessity. The 2009 Act and Bush’s earlier measures transformed them into tribunals of convenience, for the statutory changes allowed military commissions to be used for trials at Guantánamo—far removed from any battlefield—for persons held years for on end, in some cases almost a decade.

Given his National Archives speech and his sponsorship of the Military Commissions Act of 2009, Obama is in no position to complain of the threat that the use of military commissions in these circumstances poses to due process. Obama’s only remaining objection to Congress’s actions is a rather limp separation of powers claim—that the December 2010 legislation barring the transfer of Guantánamo prisoners to the United States constituted an improper interference with executive prerogatives. However, if we assume, as Obama posits, that due process does not bar the use of military commissions, it is not clear why the choice of tribunal—federal civilian court versus military commission—should be entrusted to the exclusive discretion of the attorney general. After all, Congress created both tribunals.

In his National Archives speech, Obama not only defended the use of military commissions, but also endorsed Bush’s policy of imprisoning suspected terrorists without providing them with a trial of any type. This policy violates a basic principle—the principle of freedom—that is rooted in due process and the protection of the writ of habeas corpus. Any person imprisoned by the United States must be charged with a crime and swiftly brought to trial. In effect, Obama, much like Bush, claimed there is an exception to this principle that allows the executive to imprison persons captured on the battlefield and to hold them for the duration of hostilities without ever affording them a trial. Yet he did not acknowledge the very special nature of the war against terrorism—a war without a readily foreseeable end—and the threat that imprisonment without trial posed to the principle of freedom and its underlying values when applied to such a war.

Obama denies that habeas is available for the prisoners of Bagram, just as Bush denied it was available for the Guantánamo prisoners.

In March 2011 Obama issued an executive order establishing a system to review periodically those being held at Guantánamo to determine whether they continue to pose a threat to the United States. This review is to be conducted by a board consisting of representatives from the Departments of State, Defense, Justice, and Homeland Security, and the Offices of the Director of National Intelligence and the Chairman of the Joint Chiefs of Staff. This board is required to act by consensus. If it determines that a prisoner no longer poses a threat to the United States, it must issue an order authorizing his transfer abroad, and the secretary of state and secretary of defense are directed to make “vigorous efforts” to arrange for the transfer. Because this handcrafted national security parole procedure is to be applied to prisoners who have never been adjudicated guilty of a crime, Obama’s executive order does not cure, but only underscores, the offense to the principle of freedom posed by his policy—first initiated by Bush—of imprisonment without trial.

Khalid Sheikh Mohammed presents an unusual case, not simply because of his role in 9/11, but also, and more importantly, because Holder had initially determined that he was to be tried and that this trial was to be held in a federal court. At first, Holder announced that the trial would be held in Manhattan. When that announcement produced a firestorm of protest—which New York Mayor Michael Bloomberg, one of Obama’s supporters, soon joined—Holder searched for an alternate venue and apparently contemplated holding the trial at a federal prison in rural Otisville, New York. Before a new site for the trial was announced, however, Congress enacted the ban on using appropriated funds for transferring any Guantánamo prisoners to the United States for any purpose, including trial. The options that then remained for Obama were: (a) the continued imprisonment of Khalid Sheikh Mohammed without trial (he had already been incarcerated for more than seven years) or (b) trial before a military commission. Given the available options, Obama chose the one that is, in my judgment, the less constitutionally offensive. Sympathy for Obama’s choice, however, should not obscure his complicity in constructing the alternatives he confronted.

Given his support for military commissions and indefinite detention without trial, Obama’s determination to close Guantánamo has become a gesture of doubtful significance. In December 2009 he followed up on his initial order promising to close Guantánamo in one year’s time and announced a plan to transfer many of the Guantánamo prisoners to a prison in Thomson, Illinois. In a similar vein, he objected to the December 2010 legislation effectively prohibiting such a transfer, and he vowed to fight for the repeal of that measure. However, once he made the decision, announced in his May 2009 National Archives speech, to use military commissions to try some of the Guantánamo prisoners and to detain others for indefinite, prolonged periods of time without affording them a trial of any type, the Guantánamo closure ceased to be of much importance. Guantánamo became an object of public controversy and was denounced during the 2008 presidential campaign not only because it was viewed as a site where prisoners had been tortured, but also because President Bush had planned to try some of the prisoners being held there before military commissions and to continue to detain others being held there without trial—precisely what Obama intends to continue doing. The objection to Guantánamo was largely an objection to these policies.

The notoriety of Guantánamo also arose because Bush had insisted that the prison lay beyond the reach of habeas corpus—by which a prisoner can challenge the legality of his detention—and successfully pressed Congress to amend the habeas statute to deny the availability of the writ to anyone determined to be an unlawful enemy combatant. The June 2008 Supreme Court decision in Boumediene v. Bush relieved Obama from having to take any position on the availability of habeas corpus for Guantánamo prisoners, for in that case, the Court upheld the constitutional right of Guantánamo detainees to the writ. Obama complied with the Court’s ruling, as Bush did, but then sought—and continues to seek—to limit its scope. In response to habeas petitions from prisoners held at Bagram Air Force Base in Afghanistan, Obama’s lawyers have argued in Al Maqaleh v. Gates that the Boumediene decision should be confined to Guantánamo and Guantánamo alone, and that the prison at Bagram—a facility maintained by the United States and one to which terrorism suspects from the four corners of the earth have been brought—lies beyond the reach of the Constitution. In taking this position, Obama has further deprived the act of closing Guantánamo of meaning.

At the time of the court proceedings in Al Maqaleh, Bagram held about 600 prisoners. The district court applied the criteria Boumediene had announced and found that habeas was available to the four petitioners there who were not Afghanistan citizens. But the court of appeals, applying these same criteria, reversed this decision and denied habeas to all of the Bagram petitioners. At this juncture the petitioners argued that they had new evidence relevant to the application of the Boumediene criteria and that this evidence further suggested that the executive had brought suspected terrorists to Bagram as a strategy for defeating any claims of habeas corpus.

The court of appeals allowed the petitioners to return to the district court. In February 2011 the district court, over the objection of Obama’s lawyers, permitted the prisoners to amend their habeas petition and thus proceed to an evidentiary hearing on their claim. Such protracted litigation is not at all surprising, given the multivariate test Justice Anthony Kennedy laid down in his opinion for the Court in Boumediene—it is nothing more than a laundry list. What is remarkable and disturbing is that today Obama denies that habeas is available for the prisoners of Bagram, just as Bush denied it was available for the Guantánamo prisoners.

Obama, rather than dismantling Bush’s counterterrorism apparatus, has in crucial respects perpetuated it. He has sought to deny habeas corpus to Bagram prisoners, endorsed the policy of imprisonment without trial, and, as vividly indicated by the turnaround with Khalid Sheikh Mohammed, continued the use of military commissions. Obama sometimes endorsed these policies with reluctance, which was never Bush’s style, but ultimately overcame this reluctance and chose to sacrifice principle. With Obama’s sanction, Bush’s counterterrorism policies have become durable features of our legal order. They have shaped our understanding of what is acceptable, and may well serve as precedents for a less reluctant president.