As the sun rises on Caprica, Starbuck (Katee Sackhoff) and Anders (Michael Trucco) discover that the Cylons have vanished. Brother Cavil declares it a miracle. But when they return to Galactica, the real reason for their survival become clear. Brother Cavil is a Cylon – his double counseled Tyrol (Aaron Douglas) – and he’s here to deliver a message: The Heroes of the Cylon – Number Six (Tricia Helfer) and Sharon (Grace Park) – have persuaded the leadership that trying to destroy the humans was an error. From now on they will live apart, in peace. At the same time, voting continues in the presidential election. Laura (Mary McDonnell) approaches Baltar (James Callis) and proposes that, whoever wins, they agree that colonization of the newly discovered planet will wait for further study. When Baltar spurns her offer, she confronts him about Number Six and, when he remains unmoved, she instructs her aide to take steps to steal the election. The plot, however, is discovered and Laura and Adama must choose between denying the will of the people and letting a man they suspect to be a Cylon collaborator take power. For Laura, the question is difficult but the answer is never in doubt. As President Baltar is sworn in, his lover, Gina, enacts a final vengeance against the fleet. Despite that, colonization of the new world goes ahead over Adama’s objections, who remains uneasy, anticipating the return of the Cylons. As the colonists set to work, Adama remains aboard Galactica with a few loyal crew, but what good is an old warhorse in time of peace? Perhaps the time has come – again – to turn out the lights...

Starbuck (Katee Sackhoff) has devised a daring plan to save the humans trapped on Caprica by using the Sharon’s (Grace Park) knowledge of Cylon navigational technology to jump a rescue mission past the Cylon defenses. On the first jump, however, one ship goes missing. The stray ship ends up floating above a blue planet that shows every sign of being able to support life. When this news reaches Galactica, it has a profound effect on the presidential race, which Baltar (James Callis) is losing badly. In a debate with President Roslin (Mary McDonnell), he goes on the offensive, using the possibility of a new home planet other than earth to attack her as a fear-monger who relies too much on religious scriptures and doesn’t care about people’s need to have solid land under their feet. Meanwhile, on the flight deck, Tyrol (Aaron Douglas) is wracked with regret after he reflexively and brutally attacks Cally (Nicki Clyne) when she wakes him from a recurrent nightmare. He consults Brother Cavil (Dean Stockwell), who divines the problem: Tyrol dreams of killing himself because he fears he is a Cylon. On Caprica, the rescue mission has found the last survivors. But even as Starbuck and Anders (Michael Trucco) embrace in a passionate reunion, the Cylons are closing in.

On Caprica, the reincarnated Number Six (Tricia Helfer) and Sharon (Grace Park) are hailed as Heroes of the Cylon for the key roles they played in the near-destruction of the human race. But these are tortured heroes. Number Six’s thoughts are haunted by Baltar (James Callis), just as she haunts his thoughts on Galactica. And Sharon has so fervently embraced her love for Tyrol (Aaron Douglas) and the fake human life the Cylons created for her undercover mission that the Cylon leadership – D’Anna (Lucy Lawless) and Doral (Matthew Bennett) – are thinking of “boxing” her (putting her consciousness into cold storage). Meanwhile, the human resistance – under the leadership of Kara’s lover, Samuel Anders (Michael Trucco) – is preparing to strike a savage blow, however futile, against the Cylon occupation. On Galactica, the captive Sharon gives premature birth to Hera, the child she conceived with Helo (Tahmoh Penikett). As the infant fights for life, she becomes the focus of intrigue, as President Roslin (Mary McDonnell) and the Cylons hidden amongst the fleet fight to gain control of this newborn symbol of hope… or harbinger of human extinction.

Two Vipers field a distress signal from an unknown source, then they suddenly vanish from the fleet's radar screens. A rescue mission is coordinated by Battlestar Pegasus, now commanded by former engine room chief Barry Garner (John Heard). Feuding with his training supervisor, Lt. Kara Thrace (Katee Sackhoff), he ignores her theory that the emergency call is a Cylon trap. Lee Adama (Jaime Bamber) is Garner's temporary XO, but when Garner bucks a direct order from Admiral William Adama (Edward James Olmos) and sends the Pegasus in pursuit of his missing Vipers, Lee is forced to act against him. Back on Galactica, a pregnant teenage stowaway has become a focal point in the presidential election campaign. Rya Kibby (Amber Rothwell) wants to exercise her legal right to an abortion. The fleet's pro-life Gemenon faction objects, threatening to pull its support for President Laura Roslin (Mary McDonnell). Recognizing that every potential life counts in a shrinking human population, Roslin considers a move that could provide the wedge issue Gaius Baltar (James Callis) needs to launch his own surprise bid for the presidency.

Fleet-wide paranoia reaches a new peak when word leaks out that the Cylon Sharon (Grace Park) is secretly being kept alive aboard Galactica. After her husband’s cruel death during a Cylon raid, Sesha Abinell (Dana Delaney) can’t stomach the` thought of a Cylon providing enemy intelligence to Galactica – she knows the Cylon is just manipulating Admiral Adama (Edward James Olmos). Assisted by three sympathizers, Sesha pulls a weapon in a bar aboard Cloud Nine and holds its occupants hostage, among them Ellen Tigh (Kate Vernon) and the uneasy romantic triangle of Apollo (Jamie Bamber), Dualla (Kandyse McClure) and Billy (Paul Campbell). Kara Thrace (Katee Sackhoff) makes a bold move to rescue the hostages that goes terribly wrong. In the end, vengeance for Sesha comes at a very high price as a much-loved human is sacrificed on her altar of vengeance.

The colonial mining ship Majahual has been working round-the-clock for a month extracting essential metals from an asteroid. The fleet has moved on, leaving Galactica behind to guard the miners from persistent Cylon raids. Their deadliest foe is an enemy Raider nicknamed Scar, the combat-savvy reincarnation of countless Cylon warriors that boasts a growing list of human kills. Hiding out in the asteroid belt, Scar is a master of hit-and-run attacks that are decimating the war-weary Viper squadrons and forcing them to throw inexperienced replacement pilots into the fray. The shaken pilots, led by Capt. Lee "Apollo" Adama (Jamie Bamber), cover their distress at the mounting casualties with a hardboiled demeanor. But neither booze nor a lustful encounter with Lee can vanquish the demons haunting Kara "Starbuck" Thrace (Katee Sackhoff). Tensions explode between Kara and Lt. Louanne “Kat” Katraine (Luciana Carro), who insists that Starbuck is dangerously off her game. A fierce competition ensues as to which of them will obliterate Scar. But when Scar traps them, Kara must suck up her pride and work with her brash nemesis in a climactic dogfight against the Cylons' top gun.

A thriving black market in food, medicine and luxury items has developed within the fleet, serving the rich and depriving the needy of essential goods. When Pegasus Commander Jack Fisk (Graham Beckel) is found brutally murdered in his private quarters amidst a cache of cigarettes, liquor and jewelry, Lee Adama (Jamie Bamber) is appointed chief investigator. Lee discovers that Fisk was fronting a racketeering operation that seemingly involves other prominent authorities. The suspects include Quorum representative Tom Zarek (Richard Hatch) and Vice President Gaius Baltar (James Callis), who is angered by President Laura Roslin's (Mary McDonnell) suggestion that he resign. The investigation turns personal for Lee when Shevon (Claudette Mink), a woman with whom he’s developed a close relationship, is kidnapped along with her young daughter by a gang of black-market thugs. Intensifying his efforts, Lee tracks Phelan (Bill Duke), the gang’s ringleader, to the Prometheus, a renegade freighter packed with contraband. During a tense standoff, he brokers a Machiavellian deal with the criminals while gaining fresh insights into human nature, including his own repressed emotions and sense of guilt.

Cancer-stricken President Laura Roslin (Mary McDonnell) lies near death in Galactica’s emergency room. Still lucid and in command, she orders that the pregnancy of the Cylon Sharon (Grace Park) be terminated when unexplainable properties are discovered in a fetal blood sample. Gaius Baltar (James Callis), who, as vice-president, is poised to take over the presidency, argues that a half-human, half-Cylon child would make an ideal case study. And the child’s father, Helo (Tahmoh Penikett), is stunned by the decision. Admiral Adama (Edward James Olmos) is determined to carry out Roslin’s final decree until Baltar discovers that the hybrid blood cells may have fantastic healing abilities. Meanwhile, an underground group of Cylon sympathizers resort to sabotage to deliver their message – humanity must broker peace with the Cylons. Adama arrests their leader, Royan Jahee (Paul Perri), but the group continues its violent rampage, bombing the tylium refinery and leaving the fleet vulnerable to enemy attack. An even more ominous threat emerges when Baltar once again connects with Gina (Tricia Helfer) – a flesh and blood version of the Cylon “Six” who lives in his head. Gina has infiltrated the sympathizers in an effort to promote the Cylon agenda. After realizing that Laura had little faith in his abilities to fill her shoes as President – and may indeed know of his affiliation with Caprica Six – Baltar discreetly arranges for a nuclear weapon to fall into the hands of Gina and the Cylon sympathizers, leaving Adama and his fleet at great risk.

The Battlestars Pegasus and Galactica go head-to-head with Cylon baseships in a battle that will change the face of the war. But for Lt. Kara "Starbuck" Thrace (Katee Sackhoff), the real war is within as she wrestles with a desperate order from Commander William Adama (Edward James Olmos). When he hears of it, Lt. Lee "Apollo" Adama (Jamie Bamber) confronts his father, challenging the order - but Commander Adama holds firm. Meanwhile, in the Pegasus brig, Pegasus crewmembers show their ugly side as they violently attack Galactica prisoners Chief Galen Tyrol (Aaron Douglas) and Lt. Karl Agathon (Tahmoh Penikett). As the battle for the Resurrection Ship intensifies, crewmembers are forced to decide how much of their humanity they are willing to sacrifice in order to survive. And the fight that begins with heroic self-sacrifice, ends in a white-knuckle test of two Commanders’ courage and character.

Lt. Kara "Starbuck" Thrace (Katee Sackhoff) prevents a potentially deadly face-off between the Battlestars Galactica and Pegasus when she arrives at the last minute bearing stunning recon photos of the Cylon “Resurrection” ship. Unable to resist this tempting target, Commander William Adama (Edward James Olmos) and Admiral Helena Cain (Michelle Forbes) establish an uneasy truce as they agree to prioritize the destruction of the “Resurrection” ship, tabling their conflicts, for now. But Adama remains distrustful, as he learns that Cain’s survive-at-all-costs attitude saw Pegasus abandon its civilian fleet months ago. Disturbed by this news, President Laura Roslin (Mary McDonnell) believes that as soon as the Resurrection Ship is destroyed, Cain will jettison Galactica’s civilian Fleet. As the power struggle continues with Cain, Adama must make an impossible decision, on the eve of a battle that could change the face of the Cylon war.