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Ali was accused of piracy for acting as a negotiator for a crew of pirates.

Ali, who was accused of piracy for acting as a translator and negotiator for a crew of pirates, was partially acquitted by a jury in November after a trial in Washington. Prosecutors initially vowed a retrial but decided last month to drop the rest of the case against him.

That’s just the kind of situation that opponents of U.S. criminal trials for Al Qaeda suspects caught abroad have long feared: The government falls short at trial — and the courts eventually order an accused terror figure freed to live legally among Americans.

“It’s a trial, not a play. You don’t know how it’s going to end,” said Cully Stimson, a former military prosecutor and defense official now at The Heritage Foundation. “Justice has all sorts of twists and turns. … It really has to be thought through at the highest level of government before we take action to bring someone here.”

One current federal terrorism prosecutor said the Ali case and the potential for his eventual release is another reason why foreign Al Qaeda suspects picked up overseas should not be brought to the United States but should instead be detained at Guantánamo or some other facility.

“It’s a significant risk … to say, ‘Oh well, we’ll just turn him over to the immigration service’” if a criminal case falls apart, said the prosecutor, who asked not to be named because he was not authorized to speak publicly. “You can’t count on the justice system working out just the way you want it to.”

Even some proponents of closing Guantánamo and relying on American civilian courts to prosecute alleged terrorists agree that the collapse of the Ali case highlights the potential downside of bringing suspected terrorists to the United States for trial.

“It really is where the rubber meets the road,” said Fordham University’s Karen Greenberg. “This is the kind of case that someone can look at and say, ‘Look how scary this is. …’ You can’t say we’re going to use [the Department of Justice] and then not be able to handle an acquittal.”

As a civilian criminal trial for Khalid Sheikh Mohammed and four other suspects in the Sept. 11 attacks was under active discussion in 2009 and 2010, Obama administration officials gave nearly ironclad assurances that the suspects would be convicted. Officials responded dismissively to congressional critics and journalists who raised questions about a backup plan if the trial didn’t go as the government expected.

“Once the administration brings detainees into the United States, it is no longer simply about what the administration will or will not do with them. It’s also about what a federal judge will or will not do,” Senate Minority Leader Mitch McConnell (R-Ky.) wrote in the National Law Journal in 2009.

When Attorney General Eric Holder announced plans to try the Sept. 11 suspects in New York — a plan later halted and reversed by the White House — he dodged questions about a possible acquittal or dismissal. “I would not have authorized the prosecution of these cases unless I was confident that our outcome would be a successful one,” he said.

Pressed by reporters to outline the government’s “Plan B,” officials then said the public could be assured that the suspects would never be released in the United States — because American immigration laws would prohibit it, because Congress has barred expenditure of funds for such a release and because the men could be returned to military custody as law-of-war detainees.

“We are confident that we have the authority to detain someone who constitutes a combatant and a threat to national security,” a senior Defense Department official said in 2009.

But now, the wind-down of the war in Afghanistan may be cutting away one of the legs of that stool.

The authority to detain individuals under the law of war is linked to the existence of ongoing armed conflict. In court, U.S. officials have repeatedly cited the Authorization for the Use of Military Force passed days after the Sept. 11 attacks as legal justification for holding prisoners at Guantánamo and elsewhere.

But President Barack Obama has vowed to end armed conflict by extricating U.S. forces from Afghanistan by the end of this year. There are serious questions about how the AUMF — which is aimed at the individuals and groups responsible for Sept. 11 — can reach the new diaspora of Al Qaeda spinoffs and Al Qaeda-inspired groups.

And in a speech last May, Obama called for revoking the 2001 war resolution entirely.

“I look forward to engaging Congress and the American people in efforts to refine, and ultimately repeal, the AUMF’s mandate. And I will not sign laws designed to expand this mandate further. Our systematic effort to dismantle terrorist organizations must continue. But this war, like all wars, must end,” the president said.

It’s a legal land mine that the administration doesn’t seem all that concerned about dodging. What many observers view as the eroding legitimacy of the AUMF is now part of the Obama administration’s campaign to close the Guantánamo Bay prison. But allowing that authority to disappear, 0r even acknowledging that’s what’s happening, would undercut the possibility of the military detention long cited as a kind of safety net if a criminal prosecution unexpectedly goes south.

“In some ways, that is kind of the elephant in the room with the AUMF and closing Guantánamo at the same time,” said American University law professor Jennifer Daskal, who served in the Justice Department’s national security division from 2009 to 2011. “If you close Guantánamo and also repeal or deem the AUMF to have expired, the question is: How do you hold these guys?”

Daskal and others say the most obvious answer to that question lies in a case the Supreme Court decided in June 2001, just months before the Sept. 11 attacks. In Zadvydas v. Davis, the justices ruled that detaining an immigrant for more than six months was usually unconstitutional unless deportation was imminent. But the majority opinion in the 5-4 case specifically left for another day the question of whether cases involving “terrorism or other special circumstances” might justify holding a foreigner in “preventive detention.”

In the event of an acquittal, authorities would “put someone in deportation proceedings and hold them pending deportation, under the assumption there will be a national security exception like the one the court alluded to in the Zadvydas opinion,” Daskal said.

Daskal acknowledged that the justices have never said outright that a suspected Al Qaeda operative could be held for a lengthy period under U.S. immigration law — but she thinks such action would be upheld.

“I’m fairly convinced that a court would find some way to determine that someone who’s an actual an ongoing threat would be held,” she said.

Human rights advocates say holding terror suspects indefinitely under immigration authority is no more tolerable than using so-called law-of-war detention that essentially treats them as prisoners of war.

“Keeping someone in indefinite detention — whether it’s immigration detention or Gitmo — is not an acceptable resolution,” Greenberg said. “We do not have a system of indefinite detention on the books — yet.”

The Ali case went off the rails for the government in the face of his claims that he was solely trying to resolve the hijacking of the M/V CEC Future — an event in which 13 crew members were held hostage for 71 days. While prosecutors contended Ali was “every bit as responsible” as those who carried weapons, the middle-aged English speaker, who had spent more than two decades in the United States, may not have seemed like an eye-patch-wearing or AK-47-toting type.

By the time of his arrest in 2011, Ali was serving as education minister for an autonomous area in Somalia. Officials lured him back to the United States by inviting him to attend an education conference. He was arrested when he landed at Dulles International Airport.

During a pretrial hearing, U.S. District Court Judge Ellen Huvelle said the case was an instance of “government overreaching” and said Ali did “not merit” a mandatory life sentence.

Ali’s defense attorney, Matthew Peed, said his client is seeking asylum in the United States because he faces danger at home as a result of defense disclosures at trial about work he did to go after pirates. “If he goes back with that having been put out there, his life will be at risk. … He really should just be let go” to live in the U.S., the lawyer said.

U.S. Immigration and Customs Enforcement spokeswoman Gillian Christensen said Ali “will remain in ICE custody until a determination has been made on his case.”

“ICE will continue to prioritize removing aliens who pose a threat to public safety or national security,” she said.

For now, the problem of what to do with a foreigner in a failed terrorism case remains theoretical, since the Justice Department has an impressive record of convictions and lengthy sentences in terrorism cases. But there has been at least one very close call.

In 2009, Obama ordered Ahmed Ghailani — a suspected plotter in the deadly attacks on U.S. embassies in Africa in 1998 — flown from Guantánamo Bay to New York to stand trial in federal court. In November 2010, a jury there convicted him on a single charge of conspiracy to destroy U.S. property and buildings, while acquitting him of the 284 other charges he faced. He ultimately received a life sentence.

Had Ghailani been acquitted on all charges, the Obama administration would have been forced to confront the question it said it never expected to arise: what to do with him. He likely could have been detained as a military prisoner for a time, but that option is looking shakier today.

While Daskal doubts a judge would ever release someone like Ghailani onto American streets, others think the odds are higher. In recent months, some judges have grown more assertive in national security-related cases, challenging the executive branch over issues like surveillance and even procedures for searching prisoners at Guantánamo. There are also questions of whether a judge would feel comfortable bucking a jury’s verdict that the government’s evidence was too weak.

“I don’t put a lot of weight into the false hope that Zadvydas will be the glue to keep a guy’s feet stuck to the ground. I don’t think it’s going to happen,” Stimson said. “The litigation milieu has changed. … We’re in a much different place. I can envision someone brought to the U.S. to stand trial being acquitted and then being granted asylum.”