I really think it needs a second episode to explain what it was all really about, how it got there, why it was there and where it went. There could be time travel, love, action thrills & spills, tears and laughter. It’d be great.
When Troy is impregnated by an entity and subsequently gives birth it's all explained at the end, when Barkley is reprogrammed in the Nth degree - explained, Night Terrors & Clues all mysteries explained. For all we know the tube thing that grows in the cargo bay is a Borg probe! One of the main characters on the holodeck was a murdering gangster! Is the life form a badly written murder mystery set loose on the Galaxy? Shouldn’t they have destroyed it when they had the chance?
I liked the idea of the ship becoming alive if not hosting an entity of some kind; I thought the entity was going to turn out to be something completely interesting.
Cause and Effect style if the Universe is one big time loop and déjà vu are distortions in the dekyon field then I send my own thought dekyon emissions to alter the timeline thus allowing this episode to make sense, once there I will create a static warp shell and collapse the nonsense.