Southern District Judge Lewis A. Kaplan yesterday ordered Ahmed Khalfan Ghailani to prison for life for his role in the al-Qaida conspiracy to bomb two U.S. embassies in East Africa in 1998.

The judge delivered the sentence after rejecting out of hand a plea for leniency by defense attorney Peter Quijano. Mr. Quijano sought a break for his client based on the claims that Mr. Ghailani had been tortured by CIA agents and had provided useful intelligence to the CIA and the fact that a jury on Nov. 17, 2010, found him guilty of only one of 285 counts—conspiracy to destroy U.S. buildings and property.

Judge Kaplan pronounced sentence after hearing emotional testimony from 11 victims and relatives of victims of the twin bombings of the embassies in Kenya and Tanzania on Aug. 7, 1998, that killed 224 people and injured thousands more.

The judge rejected the defense theory that Mr. Ghailani, 36, was a dupe who did not learn until it was too late that a truck, gas tanks, detonators and dynamite he helped obtain or assemble were intended for an Osama bin Laden-inspired attack on U.S. interests.

“I am not persuaded that Mr. Ghailani is the harmless and innocent person who has been put forward,” Judge Kaplan said. “Not at all.”

Judge Kaplan said Mr. Ghailani was involved in “cold-blooded killing and maiming of innocent people on an enormous scale. The very purpose of the crime was to create terror through death and destruction on a scale that was hard to imagine in 1998.”

Mr. Ghailani, dressed in a blue check shirt and gray slacks, listened to the testimony of the victim witnesses with his eyes closed and his head down, his hands holding on to the edge of the defense table.

The sentence brings to a close a 12-year journey for Mr. Ghailani that began with his escape from Kenya with senior al-Qaida operatives the day before the bombings, his flight to Pakistan and then his travels to Afghanistan, where he served as a cook and bodyguard for Osama bin Laden and forged documents for al-Qaida.

He was captured in Pakistan in 2004 and interrogated at a CIA black site. He was ultimately transferred to Guantánamo Bay, where he was held until 2009, when he became the first detainee to be transferred to an Article III court and actually go to trial.

Mr. Ghailani’s case was seen by many as a test of the civilian justice system’s ability to handle terrorism cases where the defendant was captured on the battlefield and the usual concerns about the search and seizure of evidence and the voluntariness of statements are complicated by the demands of intelligence gathering and the need to protect classified information and sources.

But the political winds have shifted since Mr. Ghailani was moved to New York in June 2009, when his case was widely viewed as a precedent for future prosecutions of Guantánamo detainees. Since then, many in Congress and local officials have voiced strong opposition for civilian trials, in particular vowing to block trials in Manhattan federal court, which sits near the site of the 9/11 attacks.

Congress last year cut off funding for bringing detainees from Guantánamo to the United States, and President Barack Obama reportedly has decided to keep the facility open and resume trials there by military commission. That makes it remote that other al-Qaida figures, such as Khalid Sheik Mohamed, the self-professed mastermind behind 9/11, will ever be tried in the Southern District.

‘Today Is About Justice’

Judge Kaplan has spent the last 18 months wrestling with the legal and practical effect of Mr. Ghailani’s capture, extended detention and interrogation. He rejected claims last year by Mr. Ghailani that his speedy trial rights were violated and the indictment against him should be dismissed because of outrageous government misconduct or the CIA’s use of “enhanced interrogation techniques.”

Yesterday, Mr. Quijano asked for a non-guidelines sentence of less than life in prison “based on the torture” committed by the CIA.

But the judge said the “question of illegality” surrounding the CIA’s conduct was not before him. In any event, the judge was not impressed with the argument.

“Whatever Mr. Ghailani suffered at the hands of the CIA and others in our government, and however unpleasant the conditions of his confinement, the impact on him pales by comparison to the suffering and the horror that he and his confederates caused,” the judge said.

While Mr. Ghailani “may have remedies for any illegal activities” by the government, Judge Kaplan said, they would not be in the form of sentencing relief.

“Today is about justice, not only for Mr. Ghailani, but for the victims of his crimes,” the judge said.

Mr. Quijano, flanked by a defense team that included Michael Bachrach and Anna Sideris, then made a last pitch on behalf of his client. He quoted the lawyers initially assigned to Mr. Ghailani when he was at Guantánamo facing trial by military commission—Marine Colonel Jeffrey Colwell and Air Force Major Richard Reiter. Both men, who were present yesterday, said their former client was not a hard-core Islamic radical or al-Qaida adherent.

Mr. Quijano then spoke of his own experience as a member of the “cynical” criminal defense bar who has learned through 30 years of practice “that I had to do certain things to enable me to do my job, including distancing myself.”

Mr. Quijano said that in his experience, and “not just” as Mr. Ghailani’s lawyer, he believes that Mr. Ghailani “is anything than what the government has depicted him as.”

Southern District Assistant U.S. Attorney Michael Farbiarz—along with his legal team of Assistant U.S. Attorneys Harry Chernoff, Nicholas Lewin and Sean Buckley—largely rested on his sentencing memorandum, speaking only briefly as he told the judge that Mr. Ghailani had engaged in a crime of “horror, brutality and terror.”

“By his actions, Ahmed Ghailani has marked himself as an enemy of society—as evil,” Mr. Farbiarz said, calling the defense that Mr. Ghailani was an al-Qaida dupe an “insult to the truth, an insult to common sense, and an insult to the victims who have come here” from Africa and throughout America.

Mr. Ghailani was facing a 20-year mandatory minimum, but the prosecution said the evidence supported a life sentence.

Judge Kaplan made it clear during a hearing last week that he did not accept the defense argument that the jury’s one finding for conviction must be set aside because it was inconsistent with the 284 acquittals. On Friday, he issued an opinion rejecting the motion to set aside the verdict, using language that showed he was more than ready to hold Mr. Ghailani responsible for the murders and sentence him to life (NYLJ Jan. 24).

After the sentencing yesterday, Southern District U.S. Attorney Preet Bharara called the case “difficult” for a number of reasons.

“Our goal all along was to hold Ghailani accountable for his heinous conduct, and, no matter the obstacles, to see to it that he would receive the punishment he deserved,” Mr. Bharara said. “Today, our goal was achieved, as Ahmed Ghailani will never again breathe free air.”

Mr. Ghailani became the fifth man convicted in the Southern District in the embassy bombing case under an indictment with Osama bin Laden as the lead defendant.

Mohamed Sadeek Odeh, Rashed Daoud Al-’Owhali, Wadih El-Hage and Khalfan Khamis Mohamed were convicted in 2001 following a trial before Judge Leonard Sand.

A sixth man named in the indictment, Mamdouh Mahmud Salim, is serving a life sentence for his 2000 attack on Metropolitan Correctional Center Officer Louis Pepe while Mr. Salim was awaiting trial before Judge Sand.

Mr. Quijano said yesterday that he and his legal team intend to appeal Mr. Ghailani’s sentence.

At the close of the hearing, before Mr. Ghailani was handcuffed and led away, Judge Kaplan praised the lawyers on all sides for a case that was tried well, efficiently and properly.

He also gave a nod to the defense team, saying Mr. Quijano and his colleagues, who also included attorney Steve Zissou at trial, performed a service that reminded him of that “great patriot” and the second president of the United States, John Adams, who before the Revolutionary War took on the unpopular job of defending British soldiers in the Boston Massacre case.

“You are part of a tradition that is older than the country,” the judge said.

He then acknowledged Colonel Colwell and Major Reiter for their defense of Mr. Ghailani at Guantánamo.

“You are a credit to your profession and your uniforms,” he said.