I think at the start Johnny is absoloutely untrustworthy, even when he doesn't want to kill V he wants to use them. By the time the VDB and Helman questlines are done I'd say he actually likes V but he's still Johnny. I can see him taking the pills for a few days and then realising he's acting just like Arasaka and takeing the blockers himself, maybe writing a really shit apology note before doing so.
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Yeah its hard to say. Certainly initially he is an asshole but you sorta have to live with him and he has his good points. He just becomes a part of your life. They did do real well atlhough I sorta hate the "very limited time" thing they did as it so patently becomes untrue as you play. I think it would have worked if they implied it might happen over the course of a few weeks or it could be a few months depending. I mean even if you raced though content it would be way to long relative to the way vic lays it out.
I'm convinced that the chip isn't fatal after all. There are at least 2 endings where V goes months without meaningful treatment and doesn't deteriorate further. I'd be willing to bet That Vs brain and the chip have reached an equilibrium where the chip can't overwrite V faster than Vs neurons are rearanging themselves into their original configuration through the simple act of being V (which isn't a magical willpower thing its just the way your brain makes connections)
that would honestly make more sense. Then the occasional episode might be when the two are rewriting the same resource or such.
I think Johnny is ultimately just Johnny. His growth throughout the game is coming to terms with the fact that he lost the fight against the corps and that the ends never really justified the means when he hurt the people close to him. He has to accept that he was always just a scared kid in an unfamiliar country desperately pretending to be hard enough to survive.
So...I think you can trust him to fuck shit up and fight the corps basically as soon as he calms down from realizing he is still alive. If it carried even a slight chance of success, I think he'd happily walk into Arasaka tower on a suicide run the minute you see him in the diner.
I don't think he'd hand your body back until you're chooms though, which is really cemented in the grave scene.