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The captain of the spaceship in Passengers suddenly comes in out of nowhere to complain about a tree being planted.Was the captain inside a pod or was he awake throughout?

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Thirty years into the journey, an asteroid collision damages the ship and causes its computer to awaken one passenger, mechanical engineer Jim Preston, 90 years too early.

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Soon after, another pod failure awakens Gus Mancuso, Chief Deck Officer.

https://en.wikipedia.org/wiki/Passengers_(2016_film)

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If you are referring to the character played by Laurence Fishburne, he was awakened by another failure, just like the main character played by Chriss Pratt. If you are asking about the captain, played by Andy Garcia, who shows up at the end, then he was awakened properly before the end of the journey and sees the whole deck covered in plants.

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The captain and the rest of the crew were woken up on schedule to take charge of the final stage of the journey. You see them all getting ready, then riding together in the elevator, presumably on their way to either open up the bridge, and is astonished to see a forest growing in the atrium, where he'd have expected to see the ship having been essentially unchanged and mothballed for all those years.

The one who appears out of now where and complains about the tree was an engineer who was also awoken by the rapidly mounting malfunctions, and as crew had the ability to open up the bridge that Chris Pratt's character had been trying to break into, but wasn't the captain.

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