While telemetry may have reported the Omega to be free of life signs, apparently telemetry don't read crazy. In the First Captain Challenge Deck the Omega's original captain is not only alive, he's pretty determined to ensure no-one else on the ship shares that state.
Having picked off his original crew with deadly ambushes and cat and mouse mind games he'll be sticking to what works, using Sinister Noises to lower crew's morale and encouraging them to Split Up. While this morale sapping divide and conquer strategy will work with weaker willed crew, for those as psychologically solid as the Pilot he'll need to get hands on. Although he can't take on groups of crew members he's more than willing to pick off stragglers with Stalking Shadows, meaning strength in numbers has new meaning in this expansion deck.
Of course crew won't just sit still and hope, well to a degree Keeping Calm and Carrying On to avoid panic will help, but ultimately they'll need to take extreme measures. The first captain may be insane and impossible to catch but he still needs to breathe, and if he can't be tracked he must have dumped his suit, so simply by Opening All Airlocks he'll suffocate. This high risk mission skips a quarter of the Challenge Deck, but if players fail to load up on personal oxygen first, or miscalculate the remaining turns that risk could go badly wrong. Whether the rescue crew are all dead or the ship's atmosphere is blasted into the vacuum of space, the first captain will have his wish,
He Will Gift You Silence.