According to emails sent to and from the former US Secretary of State, Hillary Clinton, the military chief of staff for the Libyan opposition was killed on orders from his own commander.

According to emails sent to and from the former US Secretary of State, Hillary Clinton, the military chief of staff for the Libyan opposition was killed on orders from his own commander.

The emails, released in June, contain answers to the question, who killed General Abdel Fattah Younes? Younes was a senior military man and former Interior Minister to Libyan leader, Muammar Gaddafi. He had defected to lead the revolutionary militias. But he and two of his aides were killed in July 2011 after being arrested by other rebel forces and his death has remained a mystery ever since.

In the Clinton emails, an unknown person replies to the question, saying that Younes was killed on orders from Mustafa Abdul Jalil, a former Justice Minister who was then the first Chairman of Libya’s National Transitional Council, or TNC.

The respondent in the emails also supplies a reason for Younes’ execution. TNC security received what they believed was reliable information indicating that Younes was secretly speaking with Gaddafi’s son, Saif al-Islam Gaddafi. These discussions involved plans for Younes and Saif al-Islam to establish a government of reconciliation that would allow Muammar Gaddafi to live in internal exile. It would also mean that the TNC would be disbanded and replaced by officials and military officers loyal to Saif and Younes, the source said.

The majority of the rebel forces may have found this easy to believe back then as they didn’t necessarily trust Younes; they thought he might have been sent by Gaddafi to infiltrate their ranks.

But this explanation is too simple, too shallow and possibly even delusional – mainly because it completely ignores the role played by Islamic extremists. According to sources in the TNC – people that were close to Younes – as well as non-Islamist rebels, this story is just a cover for the real motives of Younes’ killers.

They believe that the leaders of the more religiously motivated militias, including extremist Islamic brigades and militias associated with the Muslim Brotherhood, in the revolution were scared of Younes. An army led by the charismatic Younes was a direct threat to their own ideological project and desire to take power after Gaddafi had been removed. They were acting as the TNC’s custodians and they saw themselves as the only alternative to the Libyan army. Additionally they wanted to take revenge on Younes for his past acts against Islamic forces when he served under Gaddafi.

At the end of May this year, Abdul Jalil wrote up his version of events on Libya’s Bawabat al-Wasat website. Basically he told of events and incidents that contradicted the information in the e-mails. There were no recordings that showed that Younes was in touch with Saif al-Islam, nor was there any other evidence that Younes was sabotaging the revolution’s efforts. After the report was published, the leaders of the Islamic militias didn’t contradict what Abdul Jalil had said.

The story most have heard about Younes’ death is that various reports from Islamist factions accused Younes of treason. The Libyan government, via a special committee, ordered Younes arrested until an investigation could be completed. The arrest was carried out by one of the more extremist Islamic militias, the Obeida Ibn al-Jarra militia, led by a notorious Islamist, Ahmed Abu Khattala.

Khattala is also thought to have been one of the organizers of the attack on the US embassy in Benghazi in 2012, during which US Ambassador, Christopher Stevens, was killed. In July 2014, Khattaba was arrested by a secret US mission in the Benghazi suburbs and flown to the US, where he faces prosecution.

Most people think that Khattaba’s group took Younes and his aides into the desert outside of Benghazi and shot them there. The brutal assassination of Younes proved to be just the start of a series of murders of official military leaders by extremist Islamist militias, who saw them as rivals for power in the new Libya.