Starscream has been repodded and the memory of him has been wiped from the crew's minds. Also a note, that we forgot to clarify on earlier: Scorpius was repodded by a Yeerked Paco during the Yeerk plot, and then Paco couldn't find the pod again when he was unYeerked. Paco told Cybil, she told her command guys and maybe Jaime and the Doctor, and that they're keeping it hush hush to not freak everyone out that the pod disappeared while keeping an eye out for him.

Eventually the ship will wipe memory of him away too.