I think I have a better idea of how Markus’ story ended...

So I found Markus’ story kind of anit-climatic in my playthrough (Connor died in Last Chance Connor which pissed me off so much. I also got Kara killed so Alice and Luther could cross the border) so I was really trying my hardest to save Markus and I was excited to see where his story would go.

In my play through he just saved a bunch of his people and that was that and apparently the androids got their freedom “for now”.

Now, I had been civilised and peaceful throughout Markus’ play through, I wish that it somehow could’ve paid off. This is how I wish the game ended Markus’ story.

The rebellion and Jericho and everything else is just a simulation. Humans want to see how far their androids will go to disobey their owners. CyberLife want to know if their androids can think for theirselves but at the same time they want to make sure that the androids aren’t capable of killing or overpowering their creators.

If Markus rebels peacefully and is a pacifist, Markus will “die” regardless of what you do. Just before the end of Markus’ final chapter alive, Cyberlife will congratulate him on his performance on this test that he was a part of all along. He will be reset and sent back to Carl or another new owner.

If Markus is violent and becomes a public terrorist, he will die regardless. Before the end of his chapter, Kamski will appear in front of a restrained Markus, as he is locked up to a machine for deactivation. Kamski will explain to Markus that it was all a simulation and that he failed the test and now he has to be deactivated.
Before he is deactivated, another Markus android appears behind Kamski. The android stares blankly at Markus as Kamski explains that this new android is a gift for a friend (Carl) and therefore creating a loop of Markus’ existence and simulated deviancy.

I’m barely a professional screen writer but it’s just a draft of how I would have liked to see it end.