January 29, 2015 "ICH" - Ali Saleh al-Marri is a convicted conspirator who entered the United States before 9/11 in order to create a dreaded sleeper cell here that might someday launch an attack on Americans similar to what we witnessed earlier this month in Paris. When the feds woke from their slumber on 9/11, they wisely began to search immigration records for persons who came here with no discernible purpose from places known to spawn terrorist groups and who had overstayed their visas. Al-Marri was one such person.

The feds arrested him, originally on the visa violation, and then, after connecting the dots, on a series of conspiracies to aid terrorist organizations here and elsewhere.

After he was arrested by the FBI in Peoria, Illinois, and while he was being held in federal custody, he was kidnapped by U.S. military officials who arrived at the lock-up purporting to possess the lawful authority to seize him, authorized by President George W. Bush himself.

Bush had signed an order declaring al-Marri an enemy combatant and directing the military to seize him from the custody of federal prosecutors and bring him to a Navy brig. In several of the numerous cases it lost, the Bush administration argued to federal courts that once it declared a person an enemy combatant, the person was stripped of all rights.

There was and is no such category in American law as enemy combatant. The Bush administration made it up from historical terminology. But the post-9/11 era was a fearful time, and most folks accepted Bush's unconstitutional stripping of rights from detained persons as a route to safety. Al-Marri would soon be stripped of more than his rights, and that would lead to less safety for the rest of us.

Al-Marri is in the news this week because he was recently released from a federal prison and returned to his native Qatar. He was involved in a prisoner swap for an innocent American couple wrongfully imprisoned there. The release of al-Marri has the neocons accusing President Obama of "letting free a known terrorist."

In our system, the president wears many hats. One is the chief federal law enforcement officer and another is the chief diplomat. In the former, he is subject to the laws Congress has written; in the latter, he is subject only to the Constitution. In the execution of foreign policy, he cannot commit a crime, of course, but if he did, he probably would not be prosecuted.

He recently secured the release of U.S. Army Sgt. Bowe Bergdahl by swapping him for five known al-Qaida leaders who had been held for 11 years without charges at the prison camp at Gitmo. Obama arguably provided aid to a terrorist organization by sending al-Qaida leaders back to their organization—a felony for which his Department of Justice has successfully prosecuted Americans whose behavior was far more benign than his own.

Yet, the courts have been loath to interfere with any president's execution of foreign policy, no matter its apparent lawlessness. The courts permitted Abraham Lincoln to use troops to rob American banks, rape American women, and burn state and federal courthouses; they permitted Woodrow Wilson to prosecute those who sang German beer hall songs in public during World War I; and they permitted FDR to execute unsuccessful German saboteurs in the U.S. without any meaningful trial.

Because al-Marri was tortured by the U.S. Navy for two years, he pleaded guilty to one low-level crime, instead of to the true conspiracies with which he was involved—and he received a reduction in his sentence commensurate with the number of days he endured the torture. The feds agreed to this because they were fearful of revealing what the Navy had done to him. He had served 87 percent of his federal sentence by the time of his release last month. The standard period of sentence service in the federal system before release is 85 percent.

The feds shot themselves in the foot on this al-Marri case. They had much evidence against him. They needn't have kept him naked, blindfolded, shackled and wearing earplugs for months. He should have been prosecuted aggressively and humanely in a federal court in Chicago or New York City, where the feds have yet to lose terror prosecutions and the trials are basically fair. Instead, after he was arrested by the FBI, kidnapped by the military and brought to a Navy brig in South Carolina, he endured a systematic, fruitless, detrimental-to-justice, rarely-heard-of-in-modern-American-history authorized prisoner abuse.

The troops who tortured al-Marri are lucky; they could have and should have been court-martialed. The authorities who ordered it should have been prosecuted. If this had been the other way round—if the FBI had kidnapped him from military custody and tortured him (this is unthinkable today)—the FBI agents would have been fired and prosecuted.

Under federal law, all convicted federal prisoners are in the custody of the president. He can pardon, release, trade, or commute a sentence for any prisoner as he sees fit. But he cannot undo the demonstrable legal mess a predecessor created by his fixation on torture.

Andrew P. Napolitano, a former judge of the Superior Court of New Jersey, is the senior judicial analyst at Fox News Channel. Judge Napolitano has written nine books on the U.S. Constitution. The most recent is Suicide Pact: The Radical Expansion of Presidential Powers and the Lethal Threat to American Liberty.