Here's more to my Donnie Hates Mona Idea!
Before I get into anything, lemme give you this clip as an example.
This is Donnie coming to a conclusion to how he felt about Karai when she was their enemy and screwed them over by leaving them to deal with her mess.
Donnie knows himself very well to come to a conclusion as strong as hatred about someone he barely knows. (Granted, there's a lot more factors to this moment.)
Donnie knows perfectly well that an enemy can't be trusted. Even in S2E18 when April tells them Karai means well and that she trusts her, Donnie only says he trusts April. Not Karai. Even though she is his long lost sister, he's not suddenly all in to trust her. Since she made it perfectly clear that they were enemies.
Not to mention the family is greatly divided on the idea of her joining them. Splinter wants her back but accepts that things might not ever be the way he wants them to turn out. Leo and potentially Mikey are the most willing to let her join them. And Raph is the most vocal about not trusting her or even wanting her back at all.
My two cents is that Donnie felt the same way as Raph, he just never voiced it because it meant too much to his father and oldest brother, and he didn't want to be harsh.
But despite his opinions, he still did what he could to help his sister.
At the very least, if all things went wrong, he had a brother to back him up.
To tell him it's okay to give up.
That it just wasn't worth it.
Raph would keep things real, the way he did when it came to his crush on April.
So let's get to Season 4 and apply my ideas.
Because of everything he's been through in Season 3, Donnie shouldn't really trust as much as he does in canon. He's been tortured one too many times for his own liking. And he's certainly not happy that Karai did most of it.
And then Earth is destroyed because they trusted an alien, trusted their ultimate enemy to help them fight said alien's species and everything went to shit. He saw his father die. His home planet is gone.
At this point, Donnie only has what's left of his family and they're the only ones he can trust in the Space Arc. He's only trusting of Fugitoid since he saved them and is helping them save Earth, and he eventually considers him part of the family.
Then comes Mona Lisa and Sal Commander, and their interaction goes very poorly.
They're hostile from the get-go. They beat them up pretty bad. They leave for dead in an avalanche. And all to get the same metal they need for their ships. (Bonus: It was MONA who suggested letting them die)
That's exactly what a lot of their Earth enemies do.
So with all those factors, the whole team has a perfectly good reason to not trust the Salamandrians. Donnie would be completely justified in disliking them.
Even with that truce they take to get off the planet, he wouldn't trust the aliens who attacked his family for a moment. Not even when they're helping each other out.
The family does it cause there's no other option.
But suddenly... Raph is acting... strangely.
He's enamored with this ferocious girl, who was so willing to kill them for the sake of honour.
For some reason, he's lowering his guard around her.
He's suddenly forgetting about everything they want to do.
Forgetting about their goal to save Earth.
In case you forgot, this is exactly how Leo acted when he first met Karai. He was being an idiot, being all too willing to trust somebody they met as an enemy.
But Raph's case is so much worse. His puppy love is down right insulting. Especially to Donnie.
This was the brother who told him he had no shot with April. That Karai should never be trusted. And here he was acting he had just met the love of his life. Being a total hypocrite.
But every time Donnie looks at Mona, he feels nothing but contempt towards her. She tried to kill his family. He would never trust her. Their next meeting is thankfully brief and he doesn't have to look at her any longer than he has to.
Being in Space is showing him that being ruthless is what they need to survive, and whether he likes it or not, Donnie has to take lives alongside his family to save Earth. He's a ninja after all.
And then... The Evil Of Dregg comes. And Mona is revealed to have sold them out. For her planet.
Just like that, everything in Donnie's body confirms that he was right. That Mona couldn't be trusted.
And he should've had his brother backing him up.
But Raph tells Mona, "I trusted you more than anyone in the galaxy."
She apologised but what good was that when it risked their planet? The lives back on Earth.
They have every reason to cut their ties.
Leave her to fight to give them time to flee.
The solution to the problem was right there.
And Raph forgives her. For betraying him.
In all fairness, they have the same goals. Save their planets.
But they never had to risk anyone's life for it.
At this point, Donnie knows what this is.
A variable. A risk. A threat.
Raph is not being himself. He would never be like this. His big brother would never risk the lives of billions - their father - again. Look at what trusting Zog did.
It was repeating right before his eyes.
But Donnie's not gonna let that happen.
Like Raph told him before... if he wants to risk the fate of their world for a girl who was willing to backstab him, better leave Donnie out of it.
And there's only one way to deal with a threat like Mona.
So when everything on Dregg's planet is resolved, and they take care of the Scorpinoids... Mona turns her back to face Raph.
Donnie takes out his naginata and gets ready to strike.