Lindh addressed the court in Alexandria, Va. emotionally for 15 minutes.
He said Osama bin laden and the al Qaida network were against the teachings of Islam and explained how he had been led to believe that the Taliban was a just an Islamic group fighting against the Russian-backed Northern Alliance. He said had he known what he knows now about the Taliban militia, he would never have joined it.
"I have become aware of the relationship between the leaders of the Taliban and Osama bin Laden's organization," Lindh said. "Bin Laden's terrorist attacks are completely against Islam, completely contrary to the conventions of jihad and without any justification whatsoever. I have never supported terrorism in any form and never would."
He also denied any role in the death of CIA agent Johnny "Mike" Spann, who was killed in a prison uprising in Afghanistan last December, when captured Taliban and Al Qaida fighters seized weapons from their Northern Alliance captors and attempted to break out from the Qala-i-Changi prison near Mazar-i-Sharif. Spann was killed and several other U.S. special forces -- who were working with the Northern Alliance and assisting in the interrogation of their prisoners -- were injured.
Addressing the court, Spann's father, Johnny Spann said Lindh's 20-year sentence was not enough.
"Forgiveness is not the same as punishment," he said, adding that he believed that Lindh had been involved in the murder of his son. But both Ellis and Assistant U.S. Attorney Randy Bellows said that there has never been any indication that Lindh was involved in Spann's killing.
"Mr. Spann, I want you to know that I would have never accepted this plea bargain if I had seen any evidence that Mr. Lindh was involved in your heroic son's murder," Ellis said at one point.
But Spann remained unconvinced and cited other witnesses and medical evidence that he claims refuted Lindh's story.
"I don't believe all the things that you have told us, Mr. Lindh," he said. "I think you know more about my son's death than you have said."
In July, Lindh pleaded guilty as part of a deal with federal prosecutors that allowed him to avoid a possible sentence of life in prison.
At the time of the plea, Ellis indicated that he would likely impose the maximum sentence, and on Friday he kept that promise, but acknowledged that he believed Lindh was taking full responsibility for his previous mistakes.
"Life, Mr. Lindh, is about making decisions," Ellis said. "And you have made a very bad one. But I also believe you have made some good choices in your life."
As part of the plea deal, Lindh dropped claims he had been tortured and mistreated by U.S. military personnel in Afghanistan and aboard two military ships during December and January.
Lindh, 21, was captured in Afghanistan by Northern Alliance soldiers during the battle for Kunduz, the Taliban's last stronghold in Northern Afghanistan. He was turned over to the U.S. military in December before being delivered to federal custody and charged with nine felony counts, including conspiring to kill Americans, aiding a terrorist group, and explosives and weapons and charges.
Speaking before Ellis back in July, Lindh admitted to having trained at two al Qaida camps and traveling to Afghanistan to fight against the Northern Alliance troops in that country's civil war. He also pleaded guilty to a new charge -- carrying explosives while in the commission of a felony -- as part of the agreement. Each of the two charges carried a maximum prison term of 10 years.
"I provided my services as a soldier to the Taliban last year from about August to December," he told Ellis in July. "In the course of doing so, I carried a rifle and two grenades. I did so knowingly and willingly knowing that it was illegal."
He repeated these claims and promised to assist the U.S. in any present and future investigations and said that he was misled and mistaken to support the organization.
"Although I thought I knew a great deal about the Taliban when I went to the front line, it's clear to me now that there were many things of which I was not aware," he said. "I made a mistake by joining the Taliban."
Monday's hearing was originally intended to be the start of a week-long examination of whether statements he made to military personnel and FBI agents -- as well as statements made before a CNN camera -- should be admitted in a trial.
Lindh allegedly told investigators he met with al Qaida leader Osama bin Laden in Afghanistan and had been offered a position as a terrorist with the militant organization. He also apparently admitted being told by al Qaida members that 20 teams of terrorists had been sent to attack the United States and Israel.
He repeatedly denied, however, any involvement in the death of CIA agent Spann, who was killed by Lindh's fellow prisoners during the prison revolt at Qala-i-Changi.
After the rebellion, a wounded Lindh was discovered by a military medic and a freelance reporter working for CNN and transferred from Northern Alliance custody to the U.S. military.
Much of the government's claim that Lindh conspired to kill Americans revolved around his presence when Spann was killed. But his lawyer insisted Lindh had never actually participated in any fighting, even when serving as a soldier.
According to Paul McNulty, U.S. attorney for the Eastern District of Virginia, the deal allows the government to collect as much information as possible from Lindh. He will be required to cooperate with investigators, take repeated polygraph examinations, and appear as a witness in any trial at which he might be needed.
While it has been unclear in the ensuing months exactly what Lindh has told prosecutors and investigators about his involvement with al Qaida, he could be asked to testify at future trials as part of his cooperation.
He also agreed not to profit from his story in any manner and was told that any future association with a terrorist group or act of terrorism would get him treated as an enemy combatant -- like those currently being held indefinitely at the U.S. naval base in Guantanamo Bay, Cuba.