While out on a routine patrol, Apollo and Starbuck are attacked by to Viper pilots. The pair had attacked them thinking the were Cylons. The female pilot scans Apollo's ship and calls off the attack when she realizes he's human. The pair then reveal themselves to be from the battlestar Pegasus. Apollo and Starbuck find this hard to believe. Having assumed the Pegasus to have been destroyed in the Battle of Molecay with the Cylons years earlier with the destruction of the Fifth Fleet.
The Pegasus is under the leadership of the legendary Commander Cain. The Pegasus' commander meets with Apollo and Starbuck, considering the event an occasion wroth celebrating. Cain informs them that the female pilot who nearly shot them down was his daughter Sheba. He also inquires after a woman he is fond of, who much to Starbuck's surprise, turns out to be Cassiopeia.
Meanwhile, the Galactica and the fleet are dead in space because of a lack of fuel. Cain and Adama meet and clash on strategy and priorities. Adama is worried about the safety of the civilians; Cain wants to attack Cylons at the nearby planet of Gamoray. Adama proposes an attack on Cylon fuel tankers instead, which Cain reluctantly agrees to.
In the attack, Cain intentionally destroys the tankers in order to get his own way. Adama sees through the ploy and relieves Cain of his command, claiming Pegasus' fuel. The Pegasus crew support Cain and get into a tense confrontation with the Galactica crew. A Cylon attack led ultimately by Baltar himself results in Adama restoring Cain to command of the Pegasus, while Cain immediately concedes that had not Adama restrained him from his proposed attack, the refugee fleet would have been doomed at that moment. The Pegasus launches a surprise attack, and catches Baltar in the crossfire...
- Big Damn Heroes: The Pegasus arrives to defend the Galactica from Baltar's attack force just before the end credits start to roll.
- The Cavalry: The Pegasus arrives just in time to take some of the heat off the Galactica during Baltar's attack.
- General Ripper: While an inherently good person (unlike his reimagined opposite sex counterpart), Cain does some very shady things in his attempts to get the Galactica's help taking Gamoray.
- Like Father, Like Daughter: In regards to Sheba, it's even said aloud by Cain himself.
- MayDecember Romance: Cassiopeia and Cain were in this sometime prior to the series.Cassiopeia: I could be your daughter as well.Cain: You could be, but you're not.
- Military Maverick: Commander Cain.
- Nice Job Fixing It, Villain!: If it wasn't for Baltar leading an attack against the Galactica, the crew of the two crews would have gone on squabbling over the latter's fuel exchange - which has been ordered by Adama.
- Not Now, Kiddo: Baltar does this to a Cylon as he is too busy relishing on the Galactica's destruction until the Pegasus shows up...Cylon: Sir, I really think you should take a look at the other Battlestar.
- Oh, Crap!: Baltar's reaction upon seeing the "other Battlestar".
- O.O.C. Is Serious Business: Baltar is almost ecstatic when he thinks he has the Galactica dead-to-rights. But when the Pegasus shows up, he quickly turns into a sputtering wreck.
- There Is Another: The Galactica crew finally meets another surviving battlestar after the massacre during the peace conference.
- Wham Episode: The discovery of the Pegasus proves that there were indeed others besides those in the fleet who survived the destruction of the twelve colonies.