Battlestar Pegasus first appears in the re-imagined series episode "Pegasus", and remains part of the series from then until the episode "Exodus, Part 2", playing a major role in the episodes "Resurrection Ship" and "The Captain's Hand".
Battlestar Pegasus is a Mercury Class Battlestar, assigned to Battlestar Group 62 of the Colonial Fleet, and commanded by Admiral Helena Cain at the time of the Cylon attack on the Twelve Colonies. Thought to have been destroyed during the attack, Pegasus escaped, and encounters Battlestar Galactica and the last survivors of the Twelve Colonies around six months after their escape from Ragnar Anchorage.
Before the fall of the Twelve Colonies, Pegasus had just docked at Scorpion Fleet Shipyards where it was due for a three-month overhaul. Many of the ship's systems were offline, including the Command Navigation Program the Cylons used to disable Colonial defences during their attack. The Cylons' opening wave hit the shipyard with several nuclear warheads, destroying five ships, including two Battlestars. Pegasus lost over 700 crew members, but survived the attack by performing a blind FTL jump. This blind jump resulted in the ship escaping immediate destruction, but risked the battlestar's possible reappearance inside a star or planetary atmosphere.
As a result of the Cylons' devastating attack on the Twelve Colonies, Admiral Cain became increasingly iron-fisted. Pegasus's Executive Officer, Colonel Jack Fisk, recalls to his Galactica counterpart, Colonel Tigh, of an incident in which Admiral Cain shot the original XO in the head in front of the crew for refusing to implement her order to attack a heavily-defended Cylon relay station. Fisk then burst into laughter, as if this claim were a joke. However, Tigh later tells Adama he is sure Fisk was telling the truth, and in Battlestar Galactica: Razor it is shown that Cain did indeed kill Belzen, replacing him with Fisk.
It is later revealed that Pegasus had encountered a small civilian refugee fleet, which Cain subsequently cannibalized for spare parts and supplies. She also press ganged civilians into her crew at gunpoint, which led to several families being murdered under Cain's orders. Eventually, she abandoned the fifteen ship fleet to fend for itself, without any FTL drives or critical supplies.
After Pegasus escaped from the shipyards, and before meeting Galactica, Pegasus had been performing repeated hit and run attacks upon Cylon forces. Pegasus had trailed a large Cylon fleet which jumped between systems with natural resources. In one of these jumps, Pegasus discovers the escaping fleet of Colonial ships protected by Galactica.
The initial rejoicing in the rag tag fleet following Pegasus's meeting with Galactica does not last long. As the senior surviving Colonial officer, Admiral Cain assumes command of the fleet, replacing Galactica's Commander William Adama. While at first assuring Adama that she would not interfere with Galacticas operations, Cain soon orders crew reassignments, withholds the delivery of supplies to the civilian fleet and sends her so-called "Cylon interrogator", Lieutenant Thorne, to question Galactica's Cylon prisoner. Lt. Thorne's interrogation and attempted rape of the Cylon model known as Sharon results in his accidental death after he is interrupted and attacked by two of the Galacticas crew, Chief Petty Officer Galen Tyrol and Lieutenant Karl "Helo" Agathon, both of whom had had relationships with Cylon copies of Sharon.
Tyrol and Agathon are arrested by Pegasus Marines and charged with killing Lt. Thorne. Cain sentences both to death after a summary trial. Receiving the news of his men's death sentences, Commander Adama orders a strike team of Colonial Marines to be sent to Pegasus to retrieve his crewmen. An armed stand off between Pegasus and the ship's complement of Mark VII Vipers against Galactica's own Mark II and Mark VII Vipers ends when Lieutenant Starbuck reappears from her (unauthorized) recon mission aboard the stealth Blackbird with photos of a mysterious Cylon ship being guarded by two Basestars. Interrogation of Pegasus' Cylon prisoner (a Number Six model named Gina) reveals that the mysterious ship is a "Resurrection Ship", a vessel that gives new bodies to dead Cylons, effectively making the Cylons fearless of death. Although Adama and Cain declare an uneasy truce in order to coordinate an attack on the Cylons, they make plans to assassinate each other, which are called off after the Resurrection Ship is destroyed. Gina escapes with the help of Baltar and kills Admiral Cain.
Colonel Jack Fisk is promoted and named Commander of Pegasus after Cain's death; he is murdered by members of a black market organization shortly thereafter. Chief Engineer Barry Garner replaces Commander Fisk as commander of Pegasus. Around this time, the two battlestars in the fleet become known as the Bucket (Galactica) and the Beast (Pegasus). Commander Garner, who is stated as an excellent engineer, but unused to command, allows Pegasus to be drawn into an ambush by three Cylon Basestars. Pegasus suffers damage to her FTL drive cooling system, thus preventing her from escaping with an FTL jump. Commander Garner, leaving the able Lee Adama to command Pegasus in the heat of the battle, sacrifices his life to repair the damage, allowing Pegasus to jump to safety.
Adama, promoted to Admiral after Cain's death, promotes his son, Major Lee Adama, to commander and gives him command of Battlestar Pegasus. As the first mission with its new commander, Pegasus is sent to search for a missing Raptor science team and comes under attack from a force of First Cylon War era fighters. Pegasus is unable to leave due to problems with its FTL drive, but quickly fixes the problems and leaves, but not before Kara Thrace shoots down an enemy fighter in the landing pod. Learning of the Guardians from Sharon "Athena" Agathon and the First Hybrid, Pegasus, accompanied by Admiral Adama (who was there when the First Hybrid was created) goes after the Guardian Basestar to destroy it and rescue the missing science crew. The mission is a success, with the Guardian Basestar and First Hybrid destroyed, but Pegasus' XO, Major Kendra Shaw, is killed destroying it. Soon after, the fleet discovers a habitable world and begins to colonize it naming it "New Caprica". Pegasus and Galactica, with skeleton crews, form an orbital defense network over the new colony. However, when the colony is discovered a year later by a Cylon fleet they are forced to abandon the colony and jump away.
Pegasus is destroyed in action during the third-season episode "Exodus, Part 2". Disobeying orders from Admiral Adama to protect the civilians that first escape the Cylon occupation in the second season episode " Lay Down Your Burdens Part ll ", Apollo leaves all of his Viper squadrons with the civilian ships, along with most of the crew. Apollo is able to divert the attention of the four Cylon Basestars attacking Galactica after FTL jumping to New Caprica. The older battlestar continues to cover the evacuation of the New Caprica colonists. This distraction allows time for Galactica's FTL drives to be repaired and the planet-bound colonists to reach their ships and escape.
One Cylon Basestar is critically damaged by Pegasus' forward main batteries as it enters the fray, drawing the fire from the Basestars. After Galactica jumps away, Pegasus (now heavily damaged and unable to escape) is locked into a suicide course, weapons systems firing automatically. The crew is evacuated to several Raptors just before Pegasus rams a Basestar, destroying it. The explosion causes the battlestar to fragment, the starboard hangar pod colliding with and destroying another Basestar.