The Cylons descend upon the re-supply mission as the Chief races to decipher the markings in the temple believed to hold The Eye of Jupiter, a sacred icon that is believed to contain a map to Earth.
Baltar plays a game of cat and mouse with Adama and the President, thinking they will kill him once they've gotten out of him what they want to know. Lee deals with his feelings for Kara, while struggling to hang on to his marriage.
When a group of refugees board Galactica with a curable illness, it becomes very mysterious when they begin to die after taking the injection they do not believe in.
The Chief and his wife get trapped in an airlock on a routine maintenance job, while the Admiral copes with his wedding anniversary and the memories of his ex-wife.
When the head of the fuel production plant holds the fleet hostage by providing unsafe fuel, he's arrested for treason, which results in the Chief sent to the ship and held responsible for getting the plant back up and running.
Besides having to deal with the loss of Kara Thrace, the crew of the Galactica is also charged with the security surrounding the trial of Dr. Baltar and his defense attorney, who is replacing one lawyer that has already been killed.