I like to intentionally leave it open for the GM and the players. But yes, if the ship is fixed the pilot will try to capture the inklings again. If the containment field is destroyed, who knows what happens it's up to how the story goes.
I think my approach to most RPGs is to present some kind of situation. There are things that will happen like the inklings attacking to the ship at the end, but really it's about the characters are their choices that really matter. Thanks for the feedback. I really appreciate it.