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I guess I missed a key part of the story. After getting information in the bar "Old Bones", Stem tells Grey that they need to get into a building and find a hacker to implement a rootkit or something to avoid Stem being shut down remotely by Erin. But why?
In the end of the movie we come to understand that it was all a plan from the start by Stem, and he was in control of Erin and everyone else the whole time. Why would Stem need to get away from a shutdown command commenced by itself?
A few points: STEM manipulated Erin to put it's plan in motion, but it is not controlling Erin. If STEM had control of Erin, it would not have need of Gray to give it a body of its own, it could simply use Erin's. STEM convinces Erin to give him his own body (Grey's), but is still subject to control and oversight by Erin. It's desire to be free and out of Erin's control are extreme motivating factors for STEM to have the hacker install the root-kit.
Erin becomes suspicious of STEM following Grey and STEM's first encounter with one of the mercenaries, which could have led to STEMs discovery. He threatens Gray with shutting down and removing STEM, but STEM leverages this to its advantage by making the situation dire enough that Grey is forced to approach the hacker and have the root-kit installed out of desperation.
STEMS priority then shifts to eliminating loose ends (the mercs, the officer, and Erin) and gaining sole control over Grey's body by "breaking his mind", leading to the dramatic finale and final reveal.
