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Paz Is a Hallucination
This is a pretty well known one, actually- you probably did know this fact. But the entire Paz storyline in Metal Gear Solid 5: The Phantom Pain never actually happened. She was a hallucination. Snake imagined the whole thing, brought on by his inability to cope with his guilt over failing to save her in Ground Zeroes. The last scene in her storyline actually makes this clear, and also retroactively explains all the irregularities in Paz’s story in The Phantom Pain, as well as explaining why this story is so separate from the rest of the game’s narrative.
