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Following the pattern of Desmond and Hugo, John probably had a flashback of the both timelines while in the coma because of what he was muttering. When Jack made a statement about believing him, which echoes his own past words, it was kinda like de-javu for Locke. Since he paused and didn't pursue Jack after that, maybe John knows about both timelines and likes the flash-sideways better, thus does not want to return to the OT. This would make him officially on MIB's side, afterall.