An angry Mohammed Agoury told The Associated Press that he was present when a group of fighters from a faction known as the February 17 Martyrs' Brigade came to Abdel Fattah Younis' operations room outside Benghazi before dawn on Wednesday and took him away with them for interrogation.
Agoury said he tried to accompany his commander, "but Younis trusted them and went alone."
"Instead, they betrayed us and killed him," he said.
The February 17 Martyrs Brigade is a group made up of hundreds of civilians who took up arms to join the rebellion. Their fighters participate in the front-line battles with Qaddafi's forces, but also act as a semi-official internal security force for the opposition. Some of its leadership comes from the Libyan Islamic Fighting Group (LEFG) that waged a campaign of violence against Qaddafi's regime in the 1990s.
Agoury said the brigade had an agenda against Younis, because he was previously Qaddafi's interior minister and was involved in the crackdown that crushed the LIFG.
Younis defected to the rebellion early in the uprising that began in February, bringing his forces into the opposition ranks — a move that at the time raised Western hopes that the uprising could succeed in forcing out the country's ruler of more than four decades. But some on the opposition side remained deeply suspicious of him because of his longtime ties to Qaddafi. "They don't trust anyone who was with Qaddafi's regime, they wanted revenge," said Agoury.
A member of the Martyr's Brigade said his group had evidence that Younis was a "traitor." He told the AP that "the evidence will come out in a few days." The brigade member spoke on condition of anonymity because he feared reprisals.
Younis' body, along with those of two colonels who were his top aides, were found on Thursday, dumped outside Benghazi. Their throats had been cut and the bodies burned.
The head of the National Transitional Council, Mustafa Abdul-Jalil, blamed "gunmen" and said one man had been arrested, but Abdul-Jalil did not say what he believed motivated the killers.
Abdul-Jalil said Younis had been "summoned" to Benghazi for questioning on a "military matter" and was killed along with two aides while en route.
But hours before the commander's death was announced, opposition military spokesman Mohammed Al-Rijali had said Younis was taken to Benghazi for "interrogation" on suspicion his family might still have ties to the Qaddafi regime, raising questions about whether he might have been assassinated by his own side.
Benghazi woke up to fierce shooting Friday morning, as the news of Younis' death spread confusion and suspicion in the city. Thousands marched in Younis' funeral procession on Friday, as men draped the opposition tricolor flag over his coffin and carried it to a cemetery, where he was buried.
Younis' son, Ashraf, broke down, crying and screaming as they lowered the body into the ground. "We want Muammar to come back! We want the green flag back!" he shouted at the crowd, betraying his frustration with the months of chaos in the country and a desire for a return to normalcy.
At the funeral, Younis' nephew Mohammad Al-Obaidi called Younis a martyr and a champion of the Libyan uprising. Younis was given a military farewell with a 300-soldier salute before being buried. The crackling of machine guns shot in the air competed with the crowds chanting.
US State Department spokesman Mark Toner said Washington was looking into the killing of Younis and had made no judgment as to who might be responsible for the attack.
But he said the assassination underscored challenges facing the NTC as it seeks to lead an eventual democratic transition in Libya.
Europe, NATO and Arab states have been divided over how far to go in trying to oust Qaddafi, and how much support to give the opposition, a mix of tribes and factions who are largely unknown quantity, both politically and militarily.
