But when the plan went up the chain of command for approval, it was killed by then-Attorney General Janet Reno.

"They came to the decision that this plan was probably too dangerous, that the loss of life on the ground would have been significant," Cloonan said. There was concern that people around the bin Laden compound would be killed."

The Secret Team

Cloonan was part of a secret team of federal investigators whose sole purpose was to apprehend the terror leader.

Like other agents, he was relishing the idea of nabbing the head of al Qaeda.

"I would have said 'Sheik bin Laden, you are under arrest. You are charged with conspiracy to kill U.S. nationals abroad,' " he said.

Starting in early 1996, a team of FBI and CIA agents was secretly sent to an unmarked office in a nondescript building off the Beltway in Alexandria, Va. It was called Alex Station, and it was the center of a U.S. government operation to capture bin Laden. Cloonan was one of 13 FBI agents from New York who was part of Alex Station.

"We were in the business of trying to find people, track them down," he said.

By early 1998, Alex Station had developed enough information through investigation and informants to get a formal criminal indictment returned against bin Laden, which would still be used if he were captured today.

Cloonan said the agents learned a great deal about al Qaeda's operations and its leaders during this time.

"We can say for the first time, this is who is running al Qaeda, this is the military committee, this is what you do when you join al Qaeda, " Cloonan said. "You raise your right hand and you pledge bayat [swear allegiance] ... to bin Laden."

But Cloonan said they were on more than just a discovery mission.

"There's no sense in getting involved in a case like this and seeking an indictment if you're not going to bring this to a logical conclusion," Cloonan said. "And that logical conclusion for us was the arrest of bin Laden."

The Compound Plan

The plan to capture bin Laden was focused on a compound in Kandahar, the stronghold of the Taliban, the Islamic militia that ruled most of Afghanistan at the time.

"We had information, pretty good information on the particular house where he was," Cloonan said.

Using a desert area outside San Antonio, Texas, similar to the terrain in Afghanistan, the Alex Station team actually practiced the short takeoff and landing that would have been necessary to carry out the mission. A plane was to fly in from Uzbekistan.

"A U.S. plane was to fly in," Cloonan said. "And he [bin Laden] would have been greeted by an FBI agent, who would have said, 'Sheik bin Laden, there is a warrant for your arrest,'" he said.

The former attorney general declined to comment to ABCNEWS' Good Morning America, saying the incident was classified.

Cloonan says Reno's decision to kill the plan was never reopened.