The ones who revolt can just fade away. Perhaps some go to other planets. Perhaps some try to get back to Earth and are, to protect the CU, killed by other species. So the "ignorant" ones - they hadn't seen the tapes? Or they just don't believe them? The Commander sinks - opportunity for major low point here, well of despair. Ah, how about, when Commander is wallowing in self-pity, those revolting people (and here I use the word with both meanings!), try to head off back to Earth and the Commander is the only one who can bring everyone, humans and other species, together to prevent this. The Commander, of course, leads from the front, saves the day, and everyone sees what a wonderful bloke he really is, not at all mad actually, and so re-instate him as Boss. Story continues...
Alright more background.
The commander is in the process of training these recruits to join the Intergalactic Defense Confederation. A band of different alien species from all over Civilized Space, who form a collective military.
The ignorant ones have seen the tapes... Where he (the commander) was brutally manhandled, raped, experimented on, his limbs cut off (he's a cyborg now, half biological half machine, which adds to their level of distrust). Obviously no man can keep a sane head in those circumstances.
But he is fighting a war inside his own head with his own PTSD. he's actually afraid of humans - for obvious reasons. He has fits. Like seizures when he has flashbacks. So he could go down mid-battle and be useless. But he doesn't let that stop him. Add to that the fact that most humans in my world have never seen a person have a fit before, and then come out of it with his nose and ears bleeding.
As I was saying. The ignorant ones have seen the tapes, but instead of feeling pity for him (like the loyal ones), they now see him as psychologically unfit to lead them. Especially after the prank...
There's actually a prank that was played on him by some of the traitors... A prank that went very....very wrong. They were going to scare him....
And he got into a violent, defensive, strangling mood mid-scare and one recruit may end up dead...or very close to dead. I'm still deciding.
So that adds.
He could, technically, choose to wave the orders he'd been given, and not train them. But again, I have trouble figuring where I'll put them.
They can't go back to Earth since the colonization project is secret. Or their memories will have to be wiped somehow.
They can't, or won't want to end up in civilizated space. Because of culture shock I suppose. The kids don't dig aliens.