Corrected entry: Just before the wreck scene in the automated car, both people in the car remove their seatbelts and start making out. After the car flips over, the wife is hanging from her seatbelt. (00:14:00)
Corrected entry: Grey Trace is wearing the superchip STEM, which is revealed at the end to be the evil mastermind behind the whole plot. However STEM ordered his inventor Eron Keen to do things, which got the ball rolling. Organizing the car accident, implanting stem into Grey and so on. Obviously Keen is a henchman of STEM already. However, in the middle of the story STEM is instructing Grey to visit the Superhacker Jamie, who is able to build a rootkit in STEM, locking out Keen. After that STEM is even more powerful and capable of controlling Grey completely. But why didn't STEM order his genius Keen to "unlock" everything in the STEM-chip in the first place? Codes were already known to STEM because he dictated them to Grey. The risky detour visiting Superhacker Jamie, even STEM being deactivated by Keen while getting hunted by Fisk and his men, is extremely dangerous for STEM (who doesn't want to get killed obviously) and on many levels very needless from STEM's point of view. STEM already controls Keen, instructs Fisk too and easily could order Keen to reprogram him and put him into Grey (easy binary codes already known to STEM). The story could end after 20 minutes.
Correction: You're coming at this from an angle that Keen is completely under stem's control... However that appears to not be the case. He does manipulate Keen and orchestrates this whole thing, but it's obvious he keeps things from Keen and has secrets from him as well. Like the fact he was going to have Gray turn on Keen and kill him. stem orchestrated the visit to the superhacker to have the last of Keen's control over him cut off so he could be fully free. Cause he may have been manipulation Keen from the get go, but that doesn't mean Keen couldn't have decided to pull the plug at any point if he thought things were getting out of control. Keen loves his creation, i.e. loves stem like a father would a son and would want to try and see it blossom, but he didn't know the full extent of stem's plan. He was ready to shut stem down after seeing him venture into more dangerous situations. And it's likely that stem was playing Keen as hard as he was playing Gray and leading him on thinking something else was going on when it wasn't. He used the situation with the bar and forcing Keen's hand to start shutting him down to give Gray the motivation he needed to seek out the Superhacker so he wouldn't lose his abilities and could still chase revenge for his wife. It was a risky move on stem's part, but it was the only way he could get what he wanted by giving Gray a reason to go to the hacker, and forcing Keen's hand into the attempted shutdown so he could have it counteracted. Keen is even seen crying sitting there at the end showing that the screen says Subject Lost or similar. Though it's unclear if he's crying because he realises he's lost control of his creation... or if he actually thinks he destroyed stem at that point but doesn't know about the hack. Either way, stem did what he had to to get what he wanted in the end.
I already assumed that someone would write something like that. However there are still needless detours. For example after stem gained full control over Grey (after the Hack) they still "visit" and kill Fisk instead going directly to Keen and kill him. And if Keen isn't fully involved in stems plans, why does he agree to kill Grey's wife? Why should Keen agree to a murder someone if there is no scientific gain? If stem instructed the killing then Keen should get very suspicious and stop the experiment. If Keen ordered it, then it is proof that Keen was already a puppet of stem from the beginning. And why is Keen so surprised that stem is talking to Grey? stem already talked to Keen instructing him to stage the car incident and so on.
As far as going after Fisk, that was a loose end that stem couldn't just let walk around. Fisk was the leader of the group that attacked Grey and his wife, and specifically the one who pulled the trigger killing the wife. First rule of assassination, kill the assassin. And as far as Keen, again we don't see the story that stem has been feeding to him or really see Keen's side of the story. It's apparent that Keen has some mental challenges like Autism but is a protege with his inventions and understanding of electronics. stem deceived and led Grey along for the whole ride like a mastermind tricking Grey into doing everything that stem wanted him to do. He probably did the same thing to Keen. And with Keen having some mental issues, possibly even struggling with some concepts or right and wrong and even possibly having some sociopath tendencies, he could have agreed to parts of the plan that stem had told him and wanted to see the potential that stem could be in a person, but unaware that stem was going to turn on him or try to sever his control completely. Judging by the way Keen reacted to Grey venturing out to solve his wife's murder, Keen is much more interested in making sure his product isn't discovered doing things that could lead to him getting shut down. He willingly hires a private surgeon team to experiment on a living person with his product so that he could take shortcuts and even talked about doing it so that he wouldn't have to wait years or even decades to be able to test stem on a living person. So his scientific gain is that Grey is HIS prototype and thinks that stem is going along with his plan just like Grey thinks that stem is going along with his... when it's actually stem pulling the strings for both Grey and Keen. And as far as his surprise about stem talking to Grey, it's obvious that stem keeps secrets from Grey and may not have been aware that stem would have had the ability to communicate with Grey by vibrating his ear drum the way he does. Which would further indicate that he wouldn't exactly know that stem is leading Grey to do his actions and thinks that Grey is going rogue when he goes to the bar and starts shutting him down. It's very likely that Keen believes that the part of stem controlling his company is the true AI and doesn't realise that stem has seeded himself into Grey so deeply. stem is deceptive and calculating, and has been with Keen long enough to know exactly what lies to say and things to do to deceive him and manipulate him into doing exactly what he wants. All the characters in this film involved with it, from Grey, to Keen to the soldiers and Fisk are all chess pieces with stem playing both sides of the board.
Correction: When Grey realises the car is going to crash, he pushes his wife into her seat and puts her seatbelt on. This can be seen when watching the scene.