On the campaign trail, President Obama pledged to close the Guantanamo Bay detention center within a year of being elected. He also vowed to reject President Bush’s Military Commissions Act, highlighting his faith in the American federal court system in dealing with terrorism.

Yet four-and-a-half years into Obama’s presidency, not only is Guantanamo Bay still open, but military commissions have been restarted. I travelled there recently to witness commission hearings for some of those responsible for 9/11, including Al Qaeda’s Khalid Sheikh Mohammed (KSM).

When President Obama was inaugurated in January 2009, the responsibility of leadership forced a rethink of his stance on military commissions. He soon concluded their use was appropriate in allowing “the protection of sensitive sources and methods of intelligence-gathering…and for the presentation of evidence gathered from the battlefield that cannot always be effectively presented in federal courts.”

This rethink was entirely sensible, as defendants have access to a whole host of rights at military commissions ensuring a fair trial. Among them are the presumption of innocence; the right to counsel and to attend their hearings; for statements obtained via torture or mistreatment not to be used; to present evidence and compel witnesses to attend in their defense; and protection against double jeopardy. The prosecution must prove guilt beyond a reasonable doubt—the highest standard of proof possible.

There are differences from federal courts, too. For example, military commissions allow the use of hearsay (as do many international courts). However, the burden of proof regarding its reliability is on the prosecution, and the ability to introduce it in court has been narrowed.

Military commissions allow the use of classified information, but only one closed session took place during the most recent hearings. It should also be remembered that classified information is used in federal courts too. Yet unlike federal courts, transcripts of proceedings in military courts are available online almost immediately.

Underpinning these safeguards put in place for a fair trial are two other important factors. One is the track record and impartiality of judges like Colonel James Pohl, who blocked President Bush’s request that Abu Ghraib prison be demolished in 2004 and then found nine soldiers there guilty of mistreating detainees.

The other is that defense counsel is extremely adversarial and competent. This is particularly important as it is not an easy job to defend their clients. KSM—bespectacled, beard dyed red with henna and dressed in military fatigues—has proudly proclaimed himself “responsible for the 9/11 operation, from A to Z.”

The lawyers’ zeal for defending their clients has led to security issues at Guantanamo. In November 2010, Mustafa al-Hawsawi’s lawyer attempted to pass him a copy of Inspire, Al Qaeda in the Arabian Peninsula’s English-language magazine. The edition in question contained instructions on how to “make a bomb in the kitchen of your mom.” Intelligence-screening personnel ensured that Inspire did not make it to al-Hawsawi.

Such dilemmas epitomize the problem for authorities at Guantanamo: how to allow effective defense of the accused, maintain the sanctity of the attorney-client privilege, and also manage security at the detention facility.

It is clearly a difficult balance, and one of the many reasons that this case will take years to resolve. The prosecution are not anticipating the full trial beginning until late 2014, and the defendants’ right to appeal a guilty verdict as high as the Supreme Court leads some at Guantanamo to speculate about the trial taking over a decade.

Even if the verdict is rubber stamped by the Supreme Court, there are some who will never accept the legitimacy of military commissions simply because they are not federal trials.

Yet American use of military commissions at times of war goes back as far as George Washington and Abraham Lincoln. These military commissions are just the latest variation on a well-established theme. And there now needs to be reconciliation with the fact that military commissions—and indefinite detention more broadly—will be an ongoing feature of America’s response to terrorism.

Even if America were to close Guantanamo Bay tomorrow, the President’s own task force concluded that there are forty-eight detainees there that are too dangerous to release but that are unprosecutable. This means that even if Guantanamo were closed, these detainees would be indefinitely detained on the U.S. mainland instead.

No administration will simply release those they believe to be grave national-security threats. Because of this, the excessive focus that human rights agencies from around the world place on Guantanamo is misleading. The detention center there is merely the most notorious manifestation of a detention policy that is here to stay.

Many will bemoan this reality in the future. However, none are likely to alter it.

Robin Simcox is a research fellow at the Henry Jackson Society.