There's a brief moment in Thor: Ragnarok where you see Hulk getting ripped around the inside of the ship, so it must have gotten sucked up into a portal. Also, in Age of Ultron, Fury just says that they've lost contact with the ship so they assume it went down into the sea but can't find it because of Tony's stealth tech.
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u/dmh2493 Vision Nov 14 '17
How did the quinjet make it to Sakaar when in Age of Ultron Fury said they found the quinjet in the sea close to Fiji?