AFP

THE charges are long overdue. Khalid Sheikh Mohammed has been in American custody since his capture in 2003. He has described himself during a military hearing as an al-Qaeda leader and friend of Osama bin Laden. He said he is responsible for a long (and somewhat baffling) list of terrorist attacks. At a hearing last year in Guantánamo Bay to assess whether he should be considered as an “enemy combatant” Mr Mohammed boasted, among other things, of planning the September 11th attacks on New York and Washington, DC, in 2001. But only now has the Pentagon charged Mr Mohammed, and five others, with murder and war crimes, for those attacks. Military prosecutors will seek the death penalty as punishment.

Despite his admissions the prosecution will be far from an open-and-shut case. Instead the planned trial will provoke many months of controversy, amid accusations of ill-treatment of inmates and the use of threats and torture—such as waterboarding, a technique that induces a feeling of drowning—to obtain confessions. Renewed demands for the closure of the detention facility at Guantánamo Bay are also expected: the leading Democratic and Republican candidates for the presidency say that they want to see the detention facility shut down.

The sorry mess of a legal system created by George Bush to deal with suspected terrorists has lurched from one failure to the next. Last June, military judges dismissed war-crimes charges against two Guantánamo inmates (a Canadian and a Yemen-born man). They decided that special military commissions could only try “unlawful” enemy combatants, whereas the accused were categorised merely as enemy fighters. Of the 778 prisoners kept in Guantánamo, fewer than 300 now remain: most of the rest have been repatriated, after long detention, without facing charges. In the six years since the creation of the military commissions only one man, David Hicks, an Australian, has been convicted, and that was the result of a plea-bargain.

Might prosecutions of these six accused succeed where other efforts have failed? Despite the confessions, important questions remain about the legitimacy of the military commissions and the ill-treatment of prisoners. The CIA recently admitted that its agents had used torture, including water-boarding of Mr Mohammed, to obtain evidence from suspects kept in secret prisons as part of its “high-value terrorist interrogation programme”. That casts doubt on the acceptability (and reliability) of earlier admissions of guilt, as five of the men now charged, including Mr Mohammed, were reportedly kept in such prisons.

Since 2006, in an effort to overcome this problem, a “clean team” of FBI investigators built a rapport with the six suspects (for example by providing ample supplies of Starbucks coffee, according to the Washington Post) and made it clear that no “rough” interrogation techniques would be used. Apparently they succeeded in gathering fresh evidence. But defence lawyers will be able to argue that previous interrogations have tainted the whole process.

And there remain severe difficulties with available resources. The decision to seek the death penalty may be understandable politically—even if it is morally unacceptable—but it means that the six defendants will each need a separate defence team of two military lawyers, an intelligence analyst and a legal support worker, according to the defence teams. With few defence lawyers available, and many opportunities to delay the trial, there is every possibility that the process will drag on long after Mr Bush leaves the White House.

Does that matter? Mr Bush's administration claims that the decision to try the six accused was made by the military authorities, not by the White House. If the trial is not over by the end of this year, an incoming president, even one who would like to see Guantánamo Bay closed quickly, is most unlikely to suspend the prosecution, however flawed. Mr Bush, too, will be content that the prosecution process keeps public attention on efforts to tackle international terrorism for the remainder of his time in office.