The first allegations against Khan became public in late 2006, when he was one of 14 top terror suspects transferred from secret CIA prisons called "black sites" to Guantanamo Bay.
The group, which also included Mohammad, was designated "high-value targets" by President George W. Bush, and held in isolation from the other detainees at the base.
Authorities said Khan had plotted to detonate the underground storage tanks of gas stations in the United States. At the time, family members rejected the idea of Khan as a terrorist.
"This is all crap — another lie from the Bush administration," his brother Ahmed Kahn told The Baltimore Sun in 2006. "He never thought of these things. It's so crazy."
Former teachers expressed shock.
"He never caused problems," said Margarita Ugarte-Caffyn, chairwoman of the English as a Second Language program at Owings Mills High School. "He always seemed like such a nice young man."
Family members described Kahn as a fun-loving brother; teachers remembered a good student.
He graduated from Owings Mills High School in 1999 and began work as a database administrator with the Maryland Office of Planning.
Also that year, Khan began attending conferences of Tablighi Jamaat, an international movement that seeks to bring Muslims closer to Islam.
Officially, the movement rejects violence, but it has been viewed by authorities as a potential recruiting ground for extremists.
Closer to home, Khan volunteered to teach database administration to youths at the Islamic Society of Baltimore, a mosque in Woodlawn. He also helped to direct traffic during Friday prayers.
While only a high school graduate, he parlayed his facility with computers into a job with Electronic Data Systems in Tysons Corner in March 2001. A certification in database software enabled him to earn $70,000 a year, the highest-paying job in the family.
The following month, his mother died.
Dixon, his attorney, says there was no single event that set Khan on the path from Baltimore County to Pakistan to Guantanamo. But authorities say he was becoming radicalized.
A month after Sept. 11, he applied to the Immigration and Naturalization Service for permission to leave the country. He said he planned to travel to Dubai to get married and to Saudi Arabia for a pilgrimage.
In fact, he traveled in January 2002 from Baltimore to Karachi, Pakistan, where a "close associate" identified in court papers as "Co-conspirator #1" introduced him as someone who could be "helpful" to al-Qaida.
There, Mohammad directed Khan in an operation that might have been a test of his loyalty. He ordered Khan to record a "martyr video," and then don an explosive vest and sit in a mosque to wait for Musharraf to arrive. Musharraf, then the president of Pakistan, never did.
While Khan was in Pakistan, he told Mohammad that has family owned gas stations in the United States.
The men discussed the plot to attack gas stations. Mohammad directed Khan to attend training on explosive device detonators and timers and, when he returned to the United States, to research the maintenance and operation of gas stations.