WHAT WE KNOW: The Scorpy-chip saved Crichton from becoming a temporary piece of toast due to the Nebari mind cleansing, when they conquered Moya for a few arns in A Clockwork Nebari. The chip is now out of Crichton's head.
WHAT I SPECULATE: Based on the evidence presented, Crichton now has NO defenses against the Nebari. The only ones left to save them are Pilot (who's stuck to Moya), Chiana, and Rygel. And Rygel took a ship and skedaddled.