The Relic isn't overwriting the body, it's overwriting V's brain - personality and memories. It doesn't alter the body itself in any shape or form, just the brain.- At the start of the game when we get the chip in our head it's basically preparing the body for a new host "Johnny" therefore the body is V's, but the brain is shared, V controls the body because Johnny doesn't want to be an ass about it and he starts understanding what's happening, but the process of writing Johnny data by the chip is still going on regardless.
This whole "prepare a body for Johnny" thing is just bad writing in my eyes. Because if you think about it, to make a suitable body for Johnny, you would need to make a perfect copy of V's brain and body a perfect copy of the original Johnny's brain and body. The relic is not capable of doing this - at all. As it is now, it's just a big plot hole than anything else, which needs a big explanation from the writers.-At the end of the game the chip practically did its job of preparing the body for Johnny so it's not V's anymore when we are in Mikoshi Alt splits Johnny and V but the body is there waiting for Johnny so Alt gives us a way out by cleaning the chip and writing everything that's left concerning V on it to make V live, but the body that is for Johnny now will consider V as an intruder "tumour" as she says.
Because it doesn't work backward. The damage is already done, the Relic is finishing its process of completely overwriting V's brain, but then Alt splits you and Johnny apart, creating Engram V to "save" your life.Now, this is where you lose me because it doesn't make any sense, when you think about it why doesn't the chip act like she did when Johnny was part of V and reverse the situation, pretty much like rewrite everything to make the body the property of V again since the consciousness of V is on the chip like Johnny at the beginning.
As for the consciousness, well, consciousness is not on the Chip. Consciousness can only be inside someone's unique physical brain - it can never leave. That's why Johnny is only but some data, that has all the memories and the entire personality of the original him - that's it.
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