Dina Temple-Raston

The appearance of Khalid Sheik Mohammed and four other men in a military courtroom at Guantanamo Bay, Cuba, ends a nearly decade-long back and forth over how best to try the men the U.S. says helped plan, pay for and execute the Sept. 11 attacks.

Khalid Sheikh Mohammed — or KSM, as he is known — has claimed that he was the mastermind of the attacks "from A to Z." But his ties to terrorism, by his own admission, go beyond that one plot. KSM saw himself as the sun around which his network revolved.

Khalid Sheikh Mohammed and four other men charged in the Sept. 11 attacks were supposed to be tried six years ago in a military tribunal created by the Bush administration.

But that system — which allowed hearsay evidence, among other things — faced questions about its fundamental fairness. When President Obama came into office, he put all the proceedings at Guantanamo on hold and asked that the commission system be revamped.

Since then, there has been an effort to make sure the trials at Guantanamo are credible, with both Congress and the Supreme Court weighing in.

The man who claims to have orchestrated the Sept. 11 attacks is expected to appear in a military courtroom this Saturday. Khalid Sheikh Mohammed and four other men are supposed to answer formal charges related to their roles in the plot.

Their arraignment will be at Guantanamo Bay, and it is the first step that leads — possibly years from now — to a military trial.

A year ago Tuesday, Navy SEALs attacked Osama bin Laden's secret compound in Pakistan and may have fundamentally changed al-Qaida as we know it.

The Obama administration's top counterterrorism chief, John Brennan, spoke Monday in Washington, D.C., and seemed on the precipice of talking about the terrorist group in the past tense.

There have been hundreds of terrorism trials in the U.S. since the attacks of Sept. 11, 2001, but the case unfolding in Brooklyn, N.Y., is different. While its focus is on defendant Adis Medunjanin and the role he allegedly played in a 2009 plot to bomb New York City subways, the trial itself breaks new ground. It marks the first time the public is hearing in open court about real al-Qaida plots from the people the terrorist group actually dispatched to carry them out.

The man accused of masterminding the bombing of the USS Cole in Yemen in 2000, Abd al-Rahim al-Nashiri, won a key battle at Guantanamo on Wednesday — a judge said he could meet with his lawyers without having to wear restraints.

In a courtroom at Guantanamo Bay on Wednesday, the man accused of masterminding the bombing of the USS Cole in 2000, Abd al-Rahim al-Nashiri, is expected to testify about the more than four years he spent in secret CIA prisons. Al-Nashiri is one of three terrorism suspects the U.S. government has admitted to waterboarding, so his testimony could be explosive. And that's why, critics argue, the government is trying to ensure that al-Nashiri's testimony be heard in secret.

The chief prosecutor for the military commissions at Guantanamo Bay, Cuba, is arguing a difficult case: that the commissions are not only fair, but can take pride of place alongside the civilian criminal justice system.

Brig. Gen. Mark Martins is the chief prosecutor for the commissions, the courts at the naval base that try high-profile terrorism suspects.

He has been called Guantanamo's detox man largely because he has made it his mission to show that the military commissions system at Guantanamo is no longer a toxic version of victor's justice.

NPR has learned that the top prosecutor at the Guantanamo Bay military commissions has asked to retire from the military after he finishes his assignment there.

Brig. Gen. Mark Martins says he hopes the decision will drain some of the politics out of the chief prosecutor's position and will provide some continuity.

There has been a subtle shift taking place in the intelligence community in recent months.

Intelligence and law enforcement officials say analysts and experts who have been tracking al-Qaida for more than a decade have been quietly reassigned. Some are being moved completely out of al-Qaida units. Others are being asked to spend less time watching al-Qaida and more time tracking more traditional foes — like state-sponsored terrorists.