By Michael Isikoff, Daniel Klaidman, and Mark Hosenball

Earlier this year, when justice Department prosecutors began trying to assemble a case against Khalid Sheikh Mohammed and four alleged co-conspirators for orchestrating the 9/11 attacks, Attorney General Eric Holder Jr. told them to make it airtight. “I cannot have a case that is not won,” Holder said, a senior Justice official tells NEWSWEEK. But the team agonized over one key question: how to prosecute the detainees without the trial being derailed by embarrassing disclosures about CIA “enhanced interrogation” techniques. For months, Justice officials say, they scoured case files for evidence “untainted” by rough interrogations or other “extralegal” methods. They were so nervous about torture allegations that they even decided against using confessions made to an FBI “clean team” that questioned the detainees after they were transferred from CIA custody to Guantánamo. The reason: prosecutors couldn’t be sure the FBI agents’ questioning wasn’t influenced by information they had previously gleaned from tough CIA treatment.

By last week, Holder and his deputies were confident they had succeeded, allowing the A.G. to announce that Mohammed and his cohorts will stand trial blocks from the former World Trade Center site. (Holder called Air Force One to inform Asia-bound White House officials of his decision, says the senior Justice official.) “There’s plenty of evidence outside of the torture stuff,” says another senior Justice official familiar with the decision who, like others interviewed, declined to be named talking about delicate deliberations. Among that evidence: wire transfers, phone records, computer files, and videos tying the defendants to the attacks.

But that doesn’t mean the trial won’t be fraught with legal skirmishes about torture—one reason some current and former U.S. spies are livid over Holder’s decision. Even if Justice can carve out a torture-free case, defense lawyers are expected to find creative ways to introduce evidence about abusive treatment, challenging the origins of every document and seeking access to CIA officers who questioned the detainees. The defense could have greater latitude to bring up torture allegations in proceedings to assess the defendants’ mental competence (lawyers for alleged co-conspirator Ramzi bin al-Shibh have already argued that their client was irreparably harmed by sedatives)—and, later on, during a possible sentencing phase when “mitigating factors” can be raised in death-penalty cases. “It borders on the incomprehensible to me,” a former senior U.S. intelligence official says about Holder’s decision. “The agency itself is going be put on trial.” Holder’s team believes it can avoid that. But even so, says a congressional aide familiar with the internal debates, “anybody who believes this is risk-free is not familiar with the process.”