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