No, none of it makes sense. Stem was in control to start with; "he" set up the attack on Grey and his wife and was talking Eron through the job of convincing Grey to allow "him" to be implanted (as seen in the flashback scenes near the end of the movie).
From what we learned at the end of the movie, the events leading up to it had to have been some game of "make pretend" that Stem was playing, which makes no sense. For example, why did Stem pretend to be under Grey's control in the first place, i.e., needing permission to take control of his body and having to obey his commands to, for example, not speak?
Logically speaking, since Stem was in control from the start, he would have taken full control of Grey immediately after he was implanted, immediately killed Eron, and then he would have gone around killing the other "upgraded" people that he wanted to eliminate.
I suspect that the twist at the end was tacked on after the story was written without going back and making changes to the story in order to make it make sense. They could have including a flashback scene during the twist reveal, showing that Eron had somehow surreptitiously hobbled Grey's Eron implant so that he and Grey had control over him (until the hacker "de-hobbled" him), though I don't know how he could have done that because Stem was already in Eron's head, as seen in the hospital flashback scene where he was talking inside Eron's head, telling him what to say to Grey.
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