"On one hand, you have our ideal of the presumption of innocence, and then you have the notion that you are dealing with people who could be - well, most likely are - guilty of terrible crimes and are our sworn enemy," she says. "How you handle that is the challenge."
So far, four minor players have been charged. None has gone to trial.
But if, as expected, formal charges are brought soon against a "high-value" detainee, perhaps even confessed 9/11 mastermind Khalid Sheikh Mohammed, much of the world's focus on Guantanamo will shift from prison camps to the courtrooms Kelly is crafting.
Two years ago, Kelly left a job she loved in Philadelphia and uprooted her struggling family to Washington to begin the job of her career, supervising a quasi-legal process that's been criticized from nearly every corner of the globe.
The 305 prisoners, most detained since 2002 as part of the U.S. military's global war on terrorism, have been held largely incommunicado, without trial, amid serious allegations of torture and mistreatment. Gitmo is a place so tainted that even Secretary of Defense Robert Gates wants it closed.
New allegations seem to surface monthly that raise serious questions about whether the trials will be fair. On Thursday, the CIA admitted destroying videotapes showing severe interrogation techniques. Such tapes might have been offered by detainees trying to prove torture.
Last week, the Supreme Court heard argument on whether the Gitmo detainees have constitutional rights - specifically habeas corpus, or access to civilian courts. A decision isn't expected for months.
"Every time you talk about Guantanamo," Kelly says, "it sets off people's buttons, either rightly because they know what's happening, or wrongly because they think they know."
Kelly's work is part logistics, part law, and she keeps two offices.
