Starbuck and Apollo are on recon patrol when they are attacked by two vipers. The vipers are about to destroy them when their leader recognizes them as Colonial and orders them to stand down. She switches to uni-com and contacts Apollo and Starbuck. When they recognize one of the pilots as BoJay who used to be in their squadron before he was transferred to the Pegasus. The leader tells them to maintain radio silence as they escort them back to the Pegasus. Apollo is amazed to see the Pegasus in front of them as it was thought to have been destroyed.
On Pegasus, Commander Cain is notified of the two pilots' capture. On the Galactica, the fleet is about out of fuel. They're picked up Cylon transmissions from a Cylon city. Adama is informed that they have lost contact with their recon patrol. On Pegasus, Apollo and Starbuck are greeted by members of Silver Spar squadron and they are filled in on what happened to the Pegasus during a battle two years earlier. Apollo and Starbuck are escorted to Commander Cain's quarters where he learns about the Galactica's situation. He announces that the Cylon empire is about to fall. On the Galactica, they are receiving what appears to be visual echo of their ship when a message comes in over Fleet Commline Alpha from Commander Cain and requests permission to come aboard.
On Galactica, Cain is welcomed by Adama whom he surprises by reuniting him with Apollo and Starbuck. He tells Adama that they were stopped by his daughter before they approached Gomorray, the Cylon's new outer capital. In Adama's quarters, he briefs him on his actions the past two years and his plans for the Cylons now that he has two battlestars. But a cautious Adama, tells him that they should concentrate their efforts at escaping the Cylons instead of fighting them. Adama wants to raid some Cylon tankers but Cain wants to attack Gomorray. He tasks Cain with coming up with a battle plan to attack the tankers. Cain asks Starbuck and Apollo to help him find a long lost love, Cassiopeia and acquaints them with his daughter, Sheba, the squadron leader who intercepted them earlier. Starbuck visits Cassiopeia and is surprised at her reaction when he reveals that Cain is alive. Cassiopeia surprises Cain in his quarters aboard Galactica and tells him that she is involved with Starbuck. In the officer's mess, Sheba and her mates are regaling the warriors with their exploits but Apollo points out that they may have to change their battle tactics. Cain enters with Cassiopeia but Sheba doesn't stick around. Cain briefs Adama and the officers on his battle plan to capture the Cylon tankers. Cain wants to use his own wings but Adama stresses that they need to work together and opts for a squadron from each ship. Apollo and Tigh are amazed at Cain's arrogance but Adama pooh-poohs the idea. Sheba learns that Cain, himself, is leading their squadron. Silver Spar and Blue squadrons launch from the Pegasus and Galactica and the Galactica's warriors are surprised to find that Cain is out there with them. Cain splits up the two squadrons as Apollo finds both Cylon tankers. As Blue squadron pursues the Cylon escort, Cain destroys first one and then the second tanker and then plays dumb as they head back.
On the Galactica, Cain tries to blame the failure of the attack on Blue squadron but uses the failure as the justification for a future attack on Gomorray. Cain urges Adama to let him begin planning an attack on Gomorray but Adama tells him to wait until the morning. As Cain and Sheba head for the Officer's Mess, Apollo tries to talk to Sheba about the failed attack but she is non-committal. In the mess, Cain incites the officer's to their eventual victory over the Cylons. The next morning, Adama, citing the likelihood of excessive casualties, decides against an attack and instead decides to take fuel from the Pegasus to distribute it around the fleet. Adama and Cain argue back and forth on the merits of the attack and orders Tigh to begin distributing the fuel but Cain refuses to allow it. Adama accuses Cain of sabotaging the tanker attack and relieves Cain of command--putting Tigh in command of the Pegasus. In the officer's mess, Cain's officers rally around him but he decries their thoughts of mutiny. On Baltar's base ship, Lucifer reports they have discovered the Galactica's fleet. Baltar notes that a single battlestar is no match for three base ships and rejects any air support from Gomorray. He decides that the Gomorray will become his seat of power. He decides to accompany the strike force that will attack the Galactica.
On Pegasus, Tigh orders the fuel distribution to begin but tensions are high as Sheba and BoJay face Apollo and Boomer as they begin the fuel distribution. Just then the alarm sounds as the Cylon task force approaches both ships. Cain acknowledges the Adama was right. Adama tells Cain to roll out the Pegasus and try to catch the attacking force between the two ships. Baltar gloats about his impending attack as the Galactica launches its fighters. Cain assumes command pf Pegasus and orders it to head out. Baltar tells his fighters to concentrate their attack on Galactica's landing bays. Baltar continues to gloat as Galactica fights for its life. On Pegasus, Cain prepares to attack. As Baltar watches the Galactica burn, the centurion informs Baltar of the other battlestar which is headed right for them.