re: Spinoff: major plot holes in movies you've noticed

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Ya, don't think it had to be a shipmate though.

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He's got to plug himself into the Nebecanezer somehow? I suppose it's remotely possible that a rouge human ship could have pulled up next to them, Cypher could have climbed on board, uploaded himself to the Matrix, but that's highly unlikely and the only other option. If it were the machines who found them, then they'd just kill them and take Morpheus alive.