Within moments, soldiers from the US Army's elite Delta Force forced him at gunpoint into a van and sped away. They'd fly him to a naval ship in the Mediterranean Sea before finally bringing him to New York to stand trial on charges of helping kill 224 people, including a dozen Americans, and wound more than 4,500.
But al-Libi, who pleaded innocent to the charges against him, wouldn't live to see his trial start Jan. 12. He died Friday night at a New York hospital of complications stemming from a recent liver surgery, his wife and authorities said Saturday. He was 50.
Al-Libi, once wanted by the FBI with a $5 million bounty on his head, was chronically ill with hepatitis C when the soldiers seized him. His wife, who asked to be identified as Um Abdullah, told The Associated Press that his experience only worsened his ailments.
"I accuse the American government of kidnapping, mistreating, and killing an innocent man. He did nothing," Um Abdullah said.
In a federal court filing Saturday, U.S. Attorney Preet Bharara said al-Libi died after being taken from New York's Metropolitan Correctional Center to a local hospital.
"Despite the care provided at the hospital, his condition deteriorated rapidly and (he) passed away," Bharara wrote.
Al-Libi, which means "of Libya" in Arabic, was his nom de guerre. Also known as Nazih Abdul-Hamed al-Ruqai, U.S. prosecutors in 2000 described al-Libi as sitting on a council that approved terrorist operations for al-Qaida, which would become infamous worldwide a year later after the Sept. 11 terror attacks.
Before that, al-Qaida's Aug. 7, 1998, truck bombings at the U.S. embassies in Nairobi, Kenya, and Dar es Salaam, Tanzania, were its deadliest assault. The bombs tore through the embassies and nearby buildings, killing 213 people and wounding some 4,500 in Kenya alone. The Tanzania attack, conducted minutes later, killed 11 people and wounded 85.
Al-Libi, believed to be a computer specialist for al-Qaida, conducted visual and photographic surveillance of the U.S. Embassy in Nairobi in late 1993, the federal court indictment against him and others alleges. In 1994, he and other al-Qaida members researched alternate potential sites in Nairobi including the local office of the U.S. Agency for International Development, as well as "British, French and Israeli targets," according to the indictment.
His path to Kenya and al-Qaida remains unclear. Al-Libi is believed to have spent time in Sudan, where Osama bin Laden was based in the early 1990s. After bin Laden was forced to leave Sudan, al-Libi turned up in Britain in 1995 where he was granted political asylum under unclear circumstances and lived in Manchester. He was arrested by Scotland Yard in 1999, but released because of lack of evidence and later fled Britain. After his indictment in December 2000 over the embassy bombings, U.S. officials said they believed he was hiding in Afghanistan.
Al-Libi later said in court filings that he returned to Libya as dissent against dictator Moammar Gadhafi grew into an open revolt that led to the leader's downfall and killing in 2011. He said he "joined with forces of NATO and the United States" to replace Gadhafi, hoping to establish a "stable Islamic secular state."
In October 2013, the U.S. Army's Delta Force swooped into Tripoli and seized al-Libi after dawn prayers, his brother Nabih al-Ruqai said. Al-Libi said the soldiers took him to the USS San Antonio, where CIA agents interrogating him warned the questioning would be the "easiest step" of three.
"I took this to mean that the physical and psychological torture would only increase if I failed to cooperate with my questioners," he said in a court affidavit. "These threats continued the entire time I was on board the ship."
Al-Libi's lawyer, Bernard Kleinman, argued his client didn't plan the bombing.
"This case involves issues much more tinged with emotion and trauma than other cases," Kleinman said in 2013. "The fact that Mr. al-Libi will be tried in New York, barely a half mile from the World Trade Center site, and that Osama bin Laden and al-Qaida will be referenced numerous times in connection with his co-defendants cannot be ignored."
Al-Libi isn't the only terror suspect to be snatched by U.S. special forces in Libya. American troops last year grabbed Ahmed Abu Khattala, a suspect in the 2012 attack on the U.S. Consulate in Benghazi that killed four Americans, including U.S. Ambassador Chris Stevens.
The ability for U.S. troops to move freely in Libya reflects the chaos gripping the country beset by rival militias and political factions in the years since Gadhafi's downfall. Battles openly rage in its east and west as Islamic militant groups have turned coastline cities and border areas into safe havens.
Libya's rival governments had no immediate reaction to al-Libi's death.
Al-Libi's wife said Saturday her husband underwent liver surgery three weeks ago, went into a brief coma and was moved prematurely back to prison. She said the last time she spoke to al-Libi, "his voice was weak and he was in a bad condition."
On Friday, she said a lawyer told her that al-Libi had been taken to a hospital and put on a ventilator.
She added: "He was dying then."
Associated Press writers Larry Neumeister in New York and Jon Gambrell contributed to this report.