– A Texas-born man suspected of being an Al-Qaida operative stood before a federal judge in Brooklyn this month. Two years earlier, his government debated whether he should be killed by a drone strike.

The denouement in the hunt for the man, Mohanad Mahmoud Al Farekh, who was arrested last year in Pakistan based on U.S. intelligence, came after a yearslong debate inside the government about whether to kill a U.S. citizen overseas without trial — an extraordinary step taken only once before, when the CIA killed the radical cleric Anwar al-Awlaki in Yemen in 2011.

Al Farekh’s court appearance comes as the Obama administration struggles to fashion new guidelines for targeted killings. The decision to use an allied intelligence service to arrest Al Farekh has bolstered a case made by some that capturing — rather than killing — terror suspects, even in some of the world’s most remote places, is more feasible than the orders for hundreds of drone strikes.

“This is an example that capturing can be done,” said Micah Zenko, of the Council on Foreign ­Relations.

The Obama administration’s discussions about the fate of Al Farekh began in earnest in 2012, and in the months that followed the CIA and the Pentagon ramped up surveillance of his movements around Pakistani tribal areas.

Drones spotted him ­several times early in 2013, and spy agencies used a warrant issued by the Federal Intelligence Surveillance Court to monitor his communications. The Pentagon nominated Al Farekh to be placed on a kill list for terrorism suspects; CIA officials also pushed for the White House to authorize his killing.

But the Justice Department, particularly Attorney General Eric Holder, was skeptical of the intelligence dossier on Al Farekh, questioning whether he posed an imminent threat to the U.S. and whether he was as significant a player in Al-Qaida as the Pentagon and the CIA described. Holder and his aides also thought it might be possible to capture Al Farekh and bring him to trial.

The discussions took place less than two years after the 2011 targeted killing of Al-Awlaki, and Justice Department officials were sensitive to the criticism leveled against them for approving that strike.

“Because he was an American citizen, we needed more information,” said one former senior official.

Another complicating factor emerged in May 2013, when the president imposed new rules for targeted killings and announced some of the rules in a speech at National Defense University.

At the time, the White House also announced that four Americans had been killed in drone strikes during Obama’s time in office — but that only Al-Awlaki had been specifically targeted. The three others had been killed in strikes aimed at others.

In a classified order, the White House directed that the Pentagon, rather than the CIA, should conduct lethal strikes against U.S. citizens suspected of terrorism. That provision was designed, at least in theory, to allow government officials to speak more freely about any operation after it had occurred.

Al Farekh’s eventual arrest has given ammunition to legal experts who say that capturing suspects is preferable.

Jameel Jaffer, deputy legal director for the ACLU, called the secret meetings about whether to kill a U.S. citizen “chilling.”