In November 2005, President George Bush signed a memorandum to Secretary of Defense Donald Rumsfeld that read

The order came a week before the administration's deadline for filing a Supreme Court brief in answer to Padilla's habeas corpus petition, and this time it was clear that the justices intended to hear the case.

The year before, in June 2004, the Justices had decided Yaser Hamdi's habeas petition, ruling that though Congress had authorized the president to detain enemy combatants captured on the Afghan battlefield, Hamdi was entitled to a fair process to challenge his enemy combatant designation; Hamdi's incommunicado detention in a naval brig had not provided such a process. “An interrogation by one's captor, however effective an intelligence-gathering tool, hardly constitutes a constitutionally adequate fact-finding before a neutral decision-maker,” Justice Sandra Day O'Connor wrote famously in the Court's plurality opinion. “We have long since made clear that a state of war is not a blank check for the President when it comes to the rights of the nation's citizens.”2 Faced with a requirement that it bring Yaser Hamdi's case before a “neutral decision-maker,” the administration had instead quietly released Hamdi in October 2004, deporting him to Saudi Arabia where he was freed on the condition he renounce his U.S. citizenship, accept a ban on travel to the U.S. and several other countries, and promise not to sue the United States over his detention.

Now it was to be Padilla's turn. His attorneys had refiled his habeas corpus petition in South Carolina against the commander of the Charleston brig, and in March 2005 a federal judge had ruled that the case was “a law enforcement matter, not a military matter” and given the government 45 days to charge him or set him free. The administration appealed directly to the Supreme Court, but the court again dodged a hearing, saying the Fourth Circuit Court of Appeals—generally considered the most conservative appellate court in the country—must review the district court's decision first. On, September 9, 2005, Judge J. Michael Luttig issued a unanimous opinion on behalf of a three-judge panel of the Fourth Circuit court that read,

Both Luttig and the administration knew the opinion would be reviewed by the Supreme Court. So to avoid a ruling that Padilla was entitled to have a hearing on whether he was the would-be apartment building and “dirty” bomber the administration had been portraying, President Bush executed the transfer order on November 20. Two days later, Attorney General Alberto Gonzales held a press conference in New York to announce that a federal court in the Southern District of Florida had returned an indictment charging Padilla “with providing—and conspiring to provide—material support to terrorists, and conspiring to murder individuals who are overseas.” Gonzales explained,

“As you know, under our criminal justice system all defendants are presumed innocent unless and until proven guilty,” Gonzales added, without a hint of irony.

The indictment of the man the administration had publicly condemned as a “bad guy” who had been apprehended on his way to carry out attacks calculated to cost scores, perhaps hundreds, of American lives made no reference whatsoever to this murderous conspiracy. Instead, Padilla and his co-defendants were now charged with operating and participating “in a North American support cell that sent money, physical assets, and mujahideen recruits to overseas conflicts for the purpose of fighting violent jihad.” The most serious charge, Count 1 of the indictment, alleged Conspiracy to Murder, Kidnap, and Maim Persons in a Foreign Country; “Beginning at a time uncertain, but no later than in or about October 1993, and continuing until on or about November 1, 2001,” the indictment read, the five defendants “did knowingly and willfully combine, conspire, confederate, and agree with others, known and unknown to the Grand Jury, to commit at any place outside the United States, acts that would constitute murder, that is, the unlawful killing of human beings with malice aforethought, kidnapping, and maiming…and did commit one or more acts within the jurisdiction of the United States, to affect the purpose and object of the conspiracy.”5

Nearly all of the group's alleged activities had taken place in the eight years preceding 9/11, and their “purpose and object” had nothing to do with the United States or its citizens; rather, the group was accused of supporting and participating in “armed confrontations in specific locations outside the United States” “for the purpose of opposing existing governments and civilian factions and establishing Islamic states under Sharia.” Over that eight-year period their countries of concern included Chechnya , Bosnia , Libya , and Somalia ; in 1998, when Padilla left the US , the group's main interest was Kosovo, where war had broken out that year. The indictment alleged that Padilla had gone to Egypt to study with financial support from the group; two years later, on July 24, 2000, he filled out a “Mujahideen Data Form,” in essence a training camp application; a few months later, the indictment asserted, phone calls intercepted in 2000 showed that Padilla had entered Afghanistan , presumably for training.

Judge Luttig—who had referred to Padilla in his opinion as someone who took up arms against the United States on behalf of al Qaeda and traveled to the U.S. to wage war on American soil—was so incensed at the indictment and the apparent arbitrariness of Padilla's treatment that he rejected the government's request to authorize Padilla's transfer to civilian custody, insisting that he should remain in the brig in order to force the Supreme Court to review his own court's decision on the scope of presidential powers. But the administration went over his head, petitioning the Supreme Court directly to grant the transfer request, and on and January 3, 2006 Padilla was released from the Charleston brig and flown to the Federal Detention Center in Miami.

In a pre-trial hearing in Miami in June, U.S. District Judge Marcia G. Cooke called the government's indictment “light on facts” and ordered prosecutors to turn over more specific information about its allegations.6 Two months later, on August 21, 2006, she dismissed the conspiracy to murder charge, ruling it duplicated the two other material support-related charges, dropping Padilla's maximum sentence if convicted from life to 15 years in prison.7 Meanwhile, with the government again seeking to avoid scrutiny of Padilla's treatment by pledging it would introduce no evidence gathered in the brig, Padilla's attorneys were pursuing two strategies to bring his interrogation into Judge Cooke's courtroom—the first an assertion that his torture he had left him unable to participate effectively in his own defense and therefore incompetent to stand trial, and the second a motion to dismiss the case for “outrageous government conduct.”

Padilla's attorneys subpoenaed Navy records and other information about his time in the brig to help build their case, and among the materials the government turned over to his attorneys were 87 videotapes of Padilla in the brig. New York Times reporter Deborah Sontag viewed a scene from one of them in early December. The recording documented a mundane event: “Today is May 21,” a voice tells the camera. “Right now we're ready to do a root canal treatment on Jose Padilla, our enemy combatant.”8 Sontag's Times story included a still frame from the video, an indelible image of Padilla in blackout goggles and headphones surrounded by three corpsmen in camouflage riot gear.9 In a subsequent NPR interview, she described what she had seen on the videotape this way:

This treatment was not disciplinary. Padilla was by all accounts a model prisoner; in an affidavit submitted in support of the motion for a mental competency hearing, attorney Andrew Patel reported that on one of his visits to the brig, the brig staff had told him that “Mr. Padilla's temperament was so docile and inactive that his behavior was like that of ‘a piece of furniture.'” Patel added, “I was also told that the Brig staff was concerned about the damage that could occur from the extended isolation that Mr. Padilla experienced in the Brig.”11

Patel, who first visited Padilla with co-counsel Donna Newman on March 3, 2004, met with his client “ten or eleven times” in the Charleston brig. During one of those meetings, Patel recalled,

“Mr. Padilla retains the belief that he will be returned to the Brig if he discusses events that occurred there,” Patel concluded. Despite repeated meetings and conversations about his defense, Patel said, “as of the date of this affirmation, Mr. Padilla remains unsure if I and the other attorneys working on his case are actually his attorneys or another component of the government's interrogation scheme.”13

To Angela Hegarty, a forensic psychiatrist who examined Padilla and submitted an affidavit in his defense, Padilla exhibited some of the characteristics associated with “Stockholm Syndrome,” the condition in which captives form intense bonds with their captors. “Mr. Padilla tends to identify with the interests of the government more than his own interests at times,” she wrote.

He also appeared concerned that he might be considered mentally ill. Hegarty found that, far from “malingering” or exaggerating his symptoms, Padilla actually “strives to present himself as stress and symptom free on interview and on testing.” “He is terrified of appearing or being seen as ‘crazy,'” she reported. “He recalled being told by one of his interrogators that if he were to relate a particular experience to someone ‘on the outside,' they would see him as ‘crazy.' He was completely unable to describe those experiences for me.”15

Though reluctant to describe his interrogation, Padilla had been willing to answer yes or no to a list of interrogation techniques Hegarty presented based on the leaked Bybee memo, and the psychiatrist told the court,

As a result of his experiences, Hegarty told the court, Padilla presented a textbook case of Post Traumatic Stress Disorder. She concluded,

A 1985 Supreme Court decision had established that for a defendant to be considered competent to stand trial, the state only needs to show that he understands the charges against him, the penalty he faces, and the adversarial nature of the proceedings, and that he is able to assist his attorneys in his defense. Padilla's attorneys concentrated on this last factor, arguing that he was too traumatized and fearful to cooperate fully in preparing his case. During the mental competency hearings, both Hegarty and a second psychiatrist testifying on behalf of the defense, Dr. Patricia Zapf, supported this conclusion. Dr. Zapf testified that Padilla was “immobilized by anxiety” and unsure whether his attorneys might not in fact be government agents; convinced he would be returned to the brig, where he would remain until he died, he was, she reported, fatalistic about the proceedings. “He'd say, ‘What does it matter? It doesn't matter. My fate has been decided. It's better to let things be.'”18

Incredibly, in the course of the competency hearing, Assistant U.S. Attorney Stephanie K. Pell revealed that the Defense Department had not turned over all of its videotapes of Padilla's interrogations to his attorneys—and that the tape it hadn't produced was the recording of Padilla's last interrogation session on March 2, 2004, the day before he was finally allowed, after almost two years in isolation, to meet with his attorneys. “We have a good faith belief the tape existed,” Pell told Judge Cooke at the hearing in February 2007, insisting the tape had been “lost” and that “an exhaustive search was conducted” but the video “could not be located.”19

“Do you understand how it might be difficult to understand that a tape related to this particular individual just got mislaid?” Judge Cooke countered.20 But there was little she could do. When Padilla's attorneys had filed notice that they planned to introduce scenes from the 87 tapes in his defense, government attorneys argued that the tapes “contain isolated, historical sideshows, meant to divert this Court's attention away from the central issue before it, which is Padilla's present ability to understand the proceedings and communicate with his counsel.” The tapes were “completely irrelevant to Padilla's present ability to communicate with his attorneys,” the government insisted; moreover, while it was understood that the classified tapes would not be played in open court, “this Court should not even consider them in the privacy of chambers,” the government insisted.21

Finally, the government argued, defense attorneys should be barred from making any reference to the conditions the tapes depicted in their cross examination of a court-appointed Bureau of Prisons psychologist who had deemed Padilla competent to stand trial.

Doing so, U.S. attorneys concluded would violate a court order on the use of classified evidence.22

Judge Cooke had ruled for the government, rejecting Padilla's petition to play portions of the tapes. Now, confronted with the fact that the government had withheld the video of Padilla's final interrogation and with its dubious claim that the tape had disappeared, his attorneys protested again. What happened during that last session with interrogators, on the day before he was allowed to meet his attorneys “directly impacts upon his relationship with his attorneys,” his lawyers argued.23 But again, though clearly troubled by the government's claim that the tape had gone missing, Judge Cooke concluded it, too, would have been inadmissible.

She did, however, allow one window into the government's treatment of Padilla in the brig. Rudolfo Buigas, the court-appointed Bureau of Prisons psychologist, had not formally examined Padilla; because Padilla had refused to submit to another psychiatric evaluation, Buigas had interviewed him for about five hours instead, and then had spoken with Sanford Seymour, the technical director of the Charleston brig, and brig psychologist Craig Noble about his state of mind in detention. Based on these interviews, Buigas had concluded that Padilla suffered from anxiety and an unnamed personality disorder, but that he was mentally fit to stand trial. Because Buigas's assessment had depended in part on their descriptions of their encounters with Padilla, Cooke ordered Seymour and Noble to testify at the hearing—though, again, they could not discuss his treatment or the conditions of his confinement, only their observations on his mental state.

During cross-examination, Seymour acknowledged that Padilla had been held in isolation with no clock or access to natural light; he said he had twice seen Padilla weeping. Noble testified that he had interviewed Padilla twice—once for a mental health intake assessment when he arrived at the brig on June 10, 2002, and the second time two years later when he had briefly spoken with Padilla not face to face, but through the hatch in his cell door through which his meals were passed. He said Padilla's health was “unremarkable” both times. Padilla's attorneys asked whether those interviews had lasted less than two minutes, as brig records suggested, but the government objected, and he was not allowed to answer because Buigas had not questioned him about the length of their discussions.24

On February 28, 2007, Judge Cooke ruled that Padilla was competent to stand trial. She explained her decision relied in large part her own observations of Padilla. Though he had arrived in her courtroom shackled, she had ordered him unbound and he had remained unshackled throughout the pre-trial hearings without incident; moreover, she had found him “keenly aware” of the court proceedings and said he “clearly has the capacity to assist his attorneys”25 She also noted that Padilla had signed an affidavit swearing to the descriptions of his treatment in the brig that his attorneys had presented, something they could not ethically have asked him to do were he incompetent. Newsweek reported that after her ruling, “Padilla, who has sat largely emotionless through the past few days of testimony about his mental competency, stood up and smiled, making a point of shaking the hands of each one of his defense attorneys.”26

Judge Cooke made clear that her decision that Padilla could stand trial on the charges before her should not be considered as a rejection of his claims of abuse during his detention in the brig. “Those claims are for another day,” she said, suggesting they would be reviewed in the course of his motion to dismiss based on “outrageous government conduct.” But like the incompetence claim, the “outrageous government conduct” motion was a legal longshot; the doctrine has been applied almost exclusively in cases of entrapment, where the government participates in or facilitates the crime for which the defendant is eventually charged. In April, Judge Cooke issued an order denying Padilla's Motion to Dismiss, finding his argument had “numerous legal infirmities” because his treatment in the brig was not connected to the present charges that prior to 9/11 he had conspired to support terrorism overseas.

She concluded:

In a footnote, however, Judge Cooke again noted that her order to deny Padilla's motion shouldn't be read as denying his assertions of abuse at the hands of the U.S. government. “This Court makes no finding with regard to Mr. Padilla's treatment at the Naval Brig. By stating that Mr. Padilla has failed to state a claim of ‘outrageous government conduct,' the Court is merely rejecting the merits of Mr. Padilla's legal argument. Within the framework of this Order, the phrase ‘outrageous government conduct' should be interpreted as a legal term of art and not defined in a conventional sense,” she wrote. 29 In another footnote, she added, “This court's holding does not imply that this is Mr. Padilla's only remedy with regard to any alleged mistreatment at the Naval Brig, only that it is the most appropriate remedy within the framework of this prosecution. Mr. Padilla is free to institute a Bivens action, an action for monetary damages or any other form of redress that he is legally entitled to pursue.”30

The trial of Jose Padilla, Adham Hassoun, and Kifah Jayyousi opened on May 14, 2007. The most serious charge against them was once again conspiracy to commit murder: in January, the 11 th Circuit Court of Appeals had reversed Judge Cooke and reinstated Count 1 of the indictment. In late June, in a show of unity that observers believed augured ill for the defense, 11 of the 12 jurors came to court dressed entirely in black; on July 3, the entire jury sat through the proceedings dressed in coordinated rows of red, white, and blue. They heard almost nothing about Padilla's time in the brig during the three-month trial; indeed, days would go by with little mention of him at all. But in closing arguments, Assistant US Attorney Brian Frazier directed the jury's attention to Padilla, Hassoun and Jayyousi's “star recruit.” The main piece of evidence against him was the “mujahadeen data form” which a disguised CIA agent testified he had found in a raid in 2001 in Afghanistan and which allegedly bore seven of Padilla's fingerprints. “You don't mail away for it” Frazier told the jury. “You are already inside the al Qaeda organization when you get this form. It was one of more than 100 times he invoked al Qaeda in a closing argument that seemed calculated to evoke the administration's early characterizations of the enemy combatant Padilla. Padilla “trained to kill,” Frazier concluded.31

On August 16, 2007, after a day and a half of deliberations, the jury returned guilty verdicts on all three main counts, including conspiracy to murder, and it was generally assumed that Padilla would be condemned to life behind bars. But on January 23, 2008, Judge Cooke announced she was sentencing him to 17 years in federal prison. She cited two factors in justifying her marked departure from federal sentencing guidelines. The first reflected her continuing discomfort with the conspiracy to murder charge. Prosecutors had presented nothing linking the defendants to specific acts of terrorism, she noted: “There is no evidence that these defendants personally maimed, kidnapped or killed anyone in the United States or elsewhere; there was never a plot to overthrow the United States government.” The second, she made clear, had to do with what she had learned about his treatment in the Charleston brig. Cooke was crediting Padilla for the three and a half years he had been held incommunicado and deprived of a mattress, clock, the Koran, or human contact, she explained. “I do find the conditions were so harsh for Mr. Padilla that they warrant consideration of the court's fashioning of a sentence in this case.”32

On January 4, 2008, Padilla's attorneys filed a lawsuit against John Yoo, the author of the so-called Bybee memos, alleging that “During his time in the military brig, Mr. Padilla was intentionally subjected to a systematic program of illegal interrogation and conditions of confinement that Defendant Yoo justified through legal opinions purporting to permit illegal conduct.”33 The Complaint alleges:

Padilla's lawsuit, which seeks a judgment declaring that abuses described in the complaint “are unlawful and violate the Constitution of the United States” and one dollar in compensatory damages, is what Judge Cooke referred to as a Bivens action, named for a Supreme Court case in which Webster Bivens successfully sued six unnamed DEA agents who had arrested him without a warrant. Yoo's attorneys moved to dismiss the case, arguing the president had the authority to authorize Padilla's detention as an enemy combatant and his interrogation, and that Yoo is entitled to immunity for his role in drafting the memos. But on June 12, 2009, U.S. District Judge Jeffrey S. White—a George W. Bush appointee—rejected those arguments and ruled that Padilla's suit can go forward.

This may well be Padilla's last opportunity to submit his treatment at the hands of the Bush administration to legal scrutiny. By transferring him from the brig to civilian custody, the administration was hoping to avoid a Supreme Court showdown over Padilla's habeas corpus petition, a showdown it knew from the Hamdi decision it was likely to lose. Yet it remained afraid that the court would take the case anyway, as a way of reviewing Judge Luttig's 4 th Circuit opinion “that the President possesses the authority under the Authorization of the Use of Military Force to detain enemy combatants who have taken up arms against the United States abroad and entered into this country for the purposes of attacking America and its citizens from within.”

But on April 3, 2006, by a 6-3 vote, the Supreme Court denied Padilla's request for review of the 4 th Circuit decision, with Justices Roberts, Stevens, Kennedy, Scalia, Thomas, and Alito holding that Padilla's petition was moot now that he was in civilian custody. Justices Ginsburg, Souter, and Breyer disagreed, with Justice Ginsberg writing in dissent,

Even some members of the majority seemed uneasy with leaving Padilla's fate so completely in the president's hands. In an opinion co-signed by Roberts and Stevens, Justice Kennedy cautioned:

But the jurist who was most outraged by the Padilla saga was Judge Michael Luttig, whose opinion, in the end, escaped Supreme Court review. When the administration asked Luttig to authorize Padilla's transfer to civilian custody, it had also asked him to withdraw his opinion, fearing that Supreme Court would hear the case even though Padilla was now to be tried in a civilian court. It was a reasonable fear: Justice Stevens, who sided with the 6-3 majority declining to hear the appeal, had previously insisted that what was “at stake in this case is nothing less than a free society.” But it was not, to Luttig, a reasonable request. In his opinion denying the request for authorization to transfer, Luttig wrote:

Luttig summarized the administration's actions in the Padilla case this way:

In a stinging conclusion, Luttig warned that such actions will inevitably have consequences “not only for the public perception of the war on terror but also for the government's credibility before the courts in litigation ancillary to that war”—and that “we cannot help but believe that those consequences have been underestimated”: