Back on Friday, June 12, 2002, the Defense Department had a big problem: Its new policy on torture of captives in the “war on terror” was about to be exposed. John Walker Lindh, the young Californian captured in Afghanistan in December 2001 and touted by John Ashcroft as an “American Taliban,” was scheduled to take the stand the following Monday in an evidence suppression hearing regarding a confession he had signed. There he would tell, under oath, about how he signed the document only after being tortured for days by US soldiers. Federal District Judge T.S. Ellis had already said he was likely to allow Lindh, at trial, to put on the stand military officers and even Guantánamo detainees who were witnesses to or participants in his alleged abuse.

The Defense Department, which we now know had in late 2001 begun a secret, presidentially approved program of torture of Afghan and Al Qaeda captives at Bagram Air Base and other locations, had made it clear to the Justice Department that it wanted the suppression hearing blocked. American torture at that point was still just a troubling rumor, and the Bush Administration clearly wanted to keep it that way. Accordingly, Michael Chertoff, who as head of the Justice Department’s criminal division was overseeing all the department’s terrorism prosecutions, had his prosecution team offer a deal. All the serious charges against Lindh–terrorism, attempted murder, conspiracy to kill Americans, etc.–would be dropped and he could plead guilty just to the technical charges of “providing assistance” to an “enemy of the U.S.” and of “carrying a weapon.” Lindh, whose attorneys dreaded his facing trial in one of the most conservative court districts in the country on the first anniversary of 9/11, had to accept a stiff twenty-year sentence, but that was half what he faced if convicted on those two minor charges alone.

But Chertoff went further, according to one of Lindh’s attorneys, George Harris. Chertoff (now an appeals court judge in New Jersey) demanded–reportedly at Defense Department insistence, according to what defense attorneys were told–that Lindh sign a statement swearing he had “not been intentionally mistreated” by his US captors and waiving any future right to claim mistreatment or torture. Further, Chertoff attached a “special administrative measure,” essentially a gag order, barring Lindh from talking about his experience for the duration of his sentence.

At the time, few paid attention to this peculiar silencing of Lindh. In retrospect, though, it seems clear that the man coasting toward confirmation as Secretary of Homeland Security effectively prevented early exposure of the Bush/Rumsfeld/Gonzales policy of torture, which we now know began in Afghanistan and later “migrated” to Guantánamo and eventually to Iraq. So anxious was Chertoff to avoid exposure in court of Lindh’s torture–which included keeping the seriously wounded and untreated Lindh, who was malnourished and dehydrated, blindfolded and duct-taped to a stretcher for days in an unheated and unlit shipping container, and repeatedly threatening him with death–that defense lawyers say he made the deal a limited-time offer. “It was good only if we accepted it before the suppression hearing,” says Harris. “They said if the hearing occurred, all deals were off.” He adds, “Chertoff himself was clearly the person at Justice to whom the line prosecutors were reporting. He was directing the whole plea agreement process, and there was at least one phone call involving him.”

“It is outrageous that Chertoff didn’t allow testimony about Lindh’s torture by American forces to come out,” says Michael Ratner, president of the Center for Constitutional Rights. “It is off the charts in terms of morality, and it should definitely be a line of questioning at Chertoff’s confirmation hearing: What did he know about Lindh’s treatment in Afghanistan, and why did he go to such lengths to silence him about it?” But that might never happen at Chertoff’s (as yet unscheduled) hearing, since the ranking Democrat on the Senate Homeland Security and Governmental Affairs Committee, Joe Lieberman, has endorsed the nomination.

Chertoff’s judicial office is referring all inquires to the White House press office. Calls there and to the Justice Department, asking for comment, were not returned.

Ratner says Chertoff’s role in the Lindh trial could well have contributed to the torture scandal that has so undermined the US effort to win over Iraqis following the invasion of their country. “Had testimony from witnesses under oath about Lindh’s torture come out in court in 2002, we might have learned about the government’s torture program earlier, and we might not have had Abu Ghraib and other torture scandals,” he says.