Wait, wait, wait. You were complaining that he survived a nuclear blast. If the issue is you don't know how he got off the ship, why didn't you just say that?
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They are one in the same. If he blows up a nuke with his bare hands how does he: A) Live B) Get off the ship (which he just nuked)
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No they aren't. You already know he's off the ship. So how surviving a nuclear blast when it's not even near him have anything to do with this? If you've played the original trilogy, the answer should be pretty obvious. Slipspace Translocation Grids are very common in large Forerunner installations. The Mantle's Approach is no exception. Even right before the fight with Chief you see him access the Translocation Grid.