Ok I'd like to talk in more details about all the issues on that part.

So, first from what the script tells us at that point.

Eron was able to access Stem. When he saw that they were walking and hunting the criminals, he'd shutdown Stem. Together with that, Stem had 2 limitations: he had to obey Gray and not be able to control the body without granted permission and could be shutdown. When the "input guard" is removed, these 2 constraints are removed.

But we see that Eron accesses a Lix terminal, and has to use shutdown app and shut the whole system down. It's very odd that they'd have a general use OS running on the chip and Stem be an app running on it, even more a conplex enough OS to have a normal user, sudo, and PAM config setting the user to execute sudo with no explicit authentication!

And also that Stem had no interface, specially a CLI, to be controlled. If Eron was able to access it in that way, he should be able to make commands it'd need to follow, to limit parts of its features, or at least to kill -9 it, instead of shutting the whole system.

It's insteresting then that the hacker was on root.

With the "input guard" removed, it showed later that Eron became unable to connect to Stem. I wonder if he was using sshd and it was disabled? :p

Now, adding the information from the final plot twist.

So we learn that Stem was controlling Eron, to the point that Eron wanted to kill Grey so he could kill Stem. We also learn that the whole action was in fact a plot from Stem to get to Eron and kill him and to get Grey to fret then get control of the head and mind.

From that we can imply that everything and anything that Stem said and did was faked. It could pretty much had lied about the input guard, starting by letting Grey think he was in control and use that as a way to let Grey aware it had control of the body without raising too much flags and still have Grey cooperating. But that can't be the case, because it's shown that Eron did access Stem and did execute shutdown. And that the hacker girl did hack Stem, otherwise she'd tell she wasn't able to. She also tells that Stem's system was restarted.

Or... was the hacker another part of Stem's plan, and the whole thing was made up, including the shutdown and restart, and Stem was faking while Grey was unable to move? That would also explain the idiotic way on how the body was moving. But then, how was Eron actually accessing Stem, and then lost control?

Ort was Eron in fact trying to hack Stem, and the use of shutdown was precisely because he had no control over it (as an app) and had to use the OS? Maybe the shutdown command in fact didn't work? Maybe the use of sudo was to suggest that Eron had access to the system but not root access, and limited sudo access? But Then how was Eron trying to hack Grey just in the time it was making up the input guard removal?

Another issue. It's clear that the thugs and even Fisk didn't know Stem was in control, as Fisk won the fight against it and it needed Grey's help to not be killed. It became a very interesting detail that Eron did hire the thugs to kill Grey and Stem, and they failed on that. I wonder if Stem didn't expect Eron would do that after it was implanted on the body.