He was gunned down on his way to answer questions about the lack of military momentum by the opposition, but reports say he was suspected of having ties to the forces of Col Muammar Gaddafi.
Gen Younes was a lifelong Gaddafi loyalist, helping the Libyan leader seize power in a coup in 1969.
As the former head of the country's Special Forces and the sitting interior minister he was the highest profile defector to the new rebel council in Benghazi and was rapidly appointed as the chief of the rebel armed forces.
But suspicions lingered about his true allegiance, fed by claims in Tripoli that there was someone on the ruling council who was in effect a double-agent.
According to the New York Times, Col Gaddafi's daughter Aisha rather mischievously refused to rule out the name of Gen Younes as the culprit in an interview she gave in April.
But it was also the lack of momentum on the battlefield and the inexplicable bit-part played by Special Forces defectors who should have had more of a leading role on the frontline that also nurtured doubts.
Some rebel fighters refused to take orders from him, giving their loyalty instead to the general's rival, the rebel commander Khalifa Hifter, who could well be named to succeed his now dead adversary.
Gaddafi contacts?Publicly Gen Younes was recalled for questioning about military operations, but there are allegations he was suspected of maintaining contacts with the Gaddafi regime.
So who killed him? Disgruntled rebel fighters, rivals looking for power or Gaddafi loyalists?
Although an arrest has been made, no names or motives have been made public and the circumstances surrounding the bodies remains unclear.
Nadia Darrez in her damaged home in the centre of MisrataIt makes for fine political theatre and it bears all the hallmarks of a Shakespearian tragedy (think Hamlet meets Macbeth).
If you are sitting in Tripoli this must be manna from heaven.
But if you are in Benghazi this is awful timing for a movement continually struggling to gain momentum on the battlefield.
And it could hardly be worse for those governments (Britain being the latest) who have staked their diplomatic credibility on the rebel government in Benghazi.
Tribal divisionsWhat matters now is the impact this has. The death taps into tribal divisions within the opposition and some members of the general's Obeidi tribe are already armed and angry at what has happened.
Just when the rebels are desperate to drive forwards on the battlefield it leaves them without a leader. And for those countries like Britain that have officially recognised the National Transitional Council as the legitimate government of Libya it feeds serious doubts and concerns about the rebels' ability to end this conflict and their ability to function as a cohesive government.
One of the main criticisms of the Nato-led operation is that it was hastily conceived without a clear strategy or exit-route. Nothing that has happened this week will allay those fears.
But the hatred of Col Gaddafi and the craving to see him overthrown may be strong enough to keep this disparate and often shambolic rebel alliance together.
No Plan BFor many, like Nadia Darrez, a young lawyer in Misrata, people have sacrificed too much and there is no going back, no Plan B.
She has been sifting through what remains of her family home on Tripoli Street, an address synonymous with the ferocious battle that took place in the city. The flat has been devastated; great holes have been punched through the walls and ceiling, the floor is littered with broken glass, masonry and bullets.
Nadia was born here. She had four brothers when this battle began. One was killed by Col Gaddafi's men. The other three are now volunteer soldiers of the rebel army.
There is little left here but anger, grief and a desire for justice.
"We need our fighters to capture him [Col Gaddafi] and all those around him and we're not going to stop this fight until this happens," she says.
What is unclear is whether that unity of purpose is enough to allow the rebels to prevail or even keep them united.
The West is frustrated by the slow progress of this conflict and whatever the facts about the mysterious death of Abdel Fatah Younes, it will give Britain and the rest of the Nato-led alliance little confidence that this five-month old conflict will end quickly or cleanly.