Things are unfolding badly on Galactica. Tigh's drinking is making him more and more unpredictable. Upon returning to Galactica he arrests Chief Tyrol and accuses him of being a Cylon, locking him up with Boomer. Cally pleads with Gaius to help clear the chief, but he refuses declaring his Cylon detection machine faulty. The new powers being wielded by the Colonel force several of the ships in the fleet to refuse Galactica any further supplies or fuel until the President has been restored. Gaius has a change of heart and sets about proving the Chief's innocence. Gaius discovers there are eight more agents hiding in the fleet while interrogating Boomer. Boomer is shot by Cally before she can be put into a newly built testing facility on Galactica. Adama awakens from his long sleep, and Galactica-Boomer begins hers.
Colonel Tigh orders attacks on all ships refusing to resupply Galactica. In the confusion four civilians are killed. The President, unable to sit by and watch this continue decides to escape with Lee, and Billy with the help of her friendly jailer and Doc Cottle. The group makes it off the ship and into hiding.
On Caprica Helo and Starbuck come under fire by a group of athletes who think they are Cylons. The misunderstanding is cleared up and Starbuck and Helo are pleased that they will have assistance to steal a ship and get off Caprica.