"Jim Bulger had her on the ground, choking her," he said.
Flemmi carried her to the basement but thought she was still alive. Flemmi wrapped a rope around her neck, put a stick in it and strangled her, Weeks said.
He said Flemmi then removed her teeth and they buried her under the dirt floor.
Hussey was one of three people who were buried in the same house after Bulger killed them, Weeks said. He said he helped moved the bodies later when the house was being sold. In 2000, after he began cooperating with the government, he led authorities to the new location in the Dorchester section of Boston.
Weeks said John McIntyre was killed after Bulger heard he may have spoken with authorities about a failed bid to send guns to the Irish Republican Army. He said McIntyre was chained to a chair and interrogated by Bulger, who held a machine gun.
After McIntyre admitted he was cooperating with law enforcement, Bugler wrapped a rope around his neck and tried to strangle McIntyre, Weeks said. The rope was too thick and the pressure caused McIntyre to vomit, he said.
"Jim says to him, 'Do you want one in the head?' and he said, 'Yes, please,'" Weeks said.
Bulger then shot him in the head, Weeks said. When that didn't kill him, Bulger shot him several more times, Weeks said.
During cross-examination, Bulger's lawyer focused largely not on the crimes Bulger is charged with, but instead on trying to get Weeks to acknowledge that Bulger loathed anyone who was a rat.
Carney asked Weeks if, during the two decades he spent working with Bulger, he made it clear that "what he hated above all else was informants."
"We killed people for being informants," Weeks said.
Carney also asked Weeks if Bulger was ever charged, despite being involved in "all manner of crimes," including extortion, loan-sharking, money-laundering and, sometimes "crimes of violence."
Weeks acknowledged that Bulger was not charged until 1995.
The defense contends that Bulger paid FBI agents, state police and local police for information on investigations so he could stay one step ahead of any indictment.
Weeks said he saw Bulger stuffing envelopes with cash at Christmas and Bulger told him the money was for various law enforcement officials, including six FBI agents he claimed he had corrupted.
Former FBI Agent John Connolly was convicted for tipping Bulger off to his 1995 indictment. Bulger fled in late 1994, just before the indictment, and was one of the nation's most wanted fugitives until he was captured in Santa Monica, Calif., in 2011.
Flemmi is serving a life sentence for 10 murders.