This question and following thoughts contains spoilers:
When you speak to the captain, if the ship is ready to depart, you get prompted to answer one of two options. One is basically 'let's go' and the other 'wait'.
Our playgroup assumed that all players, including the agent, must be aboard in order to select the 'go' option. Is this correct? Or does it keep track of the agent by itself, like it sort of does with the evidence, leading to different outcomes?
The prompt could in either case be a bit clarified with explanations within paranthesis.