Mass Effect 2 Discussion
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Shepard's implants, judging from what I read on the Wiki page, are more passive (i.e. don't control any bodily fuction) that exist mainly to hold him together. They also The only way that way I see him getting controlled is if there was a control chip implanted; that idea was vetoed by the Illusive Man though not for fear of Shepard getting controlled by an entity other than Cerberus.
shephard's implants were purely for cellular regeneration. converting dead cells and tissues into living ones by Project Lazarus. not for control.
As for the reaper IFF, I have a few counterpoints.
1. The IFF had a virus that infected the Normandy's systems. It was not broadcasted. The virus was also killed when EDI was unlocked and given access to more of the ship's systems.
2. If it was that easy for the Collectors to infect ships, then why didn't the collector ship immobilize the original Normandy? Yes, the attack on the original Normandy was to destroy it, and the second was to capture the crew. Still, since they are controlled by a machine that favors efficiency, they would prefer to shot a target that doesn't move.
Your idea about Shepard getting infected through the Collector swarms has merit if the implants, as saurabhfzd said, were meant to do anything other than help bring him back to life. The Illusive Man wanted Shepard exactly the way he was before he died; that means no implants that increase his strength or make him a super soldier. The only change made is the type of biotic implant used.
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