After you return to the escape pod bay with Olivia, Ethan tells you to take Olivia and run to the escape pod while Olivia tells you to take Ethan. At this point, you may choose either one depending on who you walk towards. If you walk towards Ethan, you take him to the pod and see Olivia get scanned. If you walk towards Olivia, you take her to the pod and see Ethan get scanned. Additionally, at the end of the first chapter, you will choose who gets to come with you on the escape pod. This choice only affects the banter between your character and the one you save. After the credits end, you will play the epilogue, and the person you left behind in the first chapter is who becomes the final Boss in the game.
