During the Cylon attack on Galactica, a Cylon scans Sam Anders in his raptor, and the Cylons break off their attack. The four Cylons agonise about their natures, and whether they might be programmed to attack, but agree to be loyal to the humans. Baltar is hustled away by a secret group, who treat him as a religious saviour, even more so after he prays aloud, offering his life in exchange for a sick boy; a colonist nearly kills Baltar for having his son shot on New Caprica, and the boy recovers. Starbuck returns, and says she has found Earth; for her, only 6 hours has passed since she disappeared, but her raptor looks brand new. There are suspicions that she may be a Cylon. Roslin determines to keep going along their current path; Starbuck insists she knows the way to Earth and that this isn't it; eventually she holds a gun to Roslin's head...
Roslin shoots Starbuck, but misses at pointblank range; Starbuck is arrested. The Cylons are divided about "reprogramming" the Raiders after them breaking off their attack; Six removes an inhibitor from the Centurions, and they rebel against the reprogrammers, killing them. The four Cylons on Galactica attempt to discover information from Baltar. Adama releases Kara from the brig and secretly gives her a ship to look for Earth.
Roslin is undergoing cancer treatment. Lee Adama is elected Caprica's representative on the Government, and challenges Roslin with the existence of a secret directive to give her powers over judges and trials. Cally discovers that Tyrol, Tigh and Tory are Cylons. She attacks Tyrol, then takes their child off to commit suicide. Tory discover hers, rescues the baby, then kills her. The resurrected Cylon leaders lead the rebel Cylons into a trap, and kill them , but outside the rage of a Resurrection ship. Kara is behaving strangely on the mission to find Earth. She admits to Sam that she feels strangely removed from reality: he eyes her speculatively.
Tory and Tigh are worried about Tyrol's behaviour at Cally's funeral service. He later makes a mistake while servicing a raptor, nearly getting the crew killed. Adama confronts him, being supportive, but he is aggressive, and ends up being demoted and reassigned. Baltar and his groupies are attacked by a fundamentalist group calling themselves "The Sons of Aquarius". In response, and egged on by his internal Six, he and his group crash a religious ceremony. Roslin visits him in the brig, and threatens him in her very calm, smiling fashion; she decrees a restriction on assembly of non-mainstream religious groups, to make sure he can't cause trouble. Lee Adama and the rest of the council overturn the decree: Lee is worried about the President abusing powers, the rest are worried that the decree will be applied to their own minority religious groups. Tigh has taken to visiting the captive Six daily.
Baltar continues growing his cult. On Kara's ship, the crew is getting restive, wanting to return to the fleet, as supplies are running low. They run across a damaged Cylon ship, and pick up a Cylon prisoner (Leoben Conoy, the model that held Starbuck captive on New Caprica [ 3.1 Occupation ]) , who tells them of they Cylon war, and that his side wants to ally with the humans to find Earth. When she orders the ship to jump to find the Cylon's mothership, her crew, led by Helo, mutinies...
... Sam backs up Kara. In the kerfuffle, Gaeta is shot in the leg. Kara agrees to take a Raptor to the Cylon base ship (along with Sam, Sharon/Athena, and Barolay); the others on Demetrius will wait until the last possible minute. They find the ship; the Sixes are hostile, but eventually agree to let Kara see the Hybrid. New Caprica Six kills Barolay, who had killed her, on New Caprica, while in the Resistance. Sam wants to kill her; Starbuck tries to talk him out of it. One of the other Sixes kills her for him: no Resurrection Ship means it is a real death. Meanwhile, back on Galactica, Roslin is undergo cancer treatment in the infirmary, and meets a dying patient who tells her of a dream of dying and seeing her family waiting; Roslin then has the same dream. Kara sees the Hybrid, who eventually says something interpretable: that the last Five know where Earth is, and that the Three (D'aana) can recognise them. They jump back to Demetrius just in time.
Kara jumps the Cylon ship back to the fleet, and the rebel Cylons and humans enter an agreement to find the Resurrection base, unbox the Three who can reveal the Five, and then destroy the base and hence the Cylons' immortality, with the Cylons being allowed to leave and take the Five with them. The humans agree, planning to renege on the deal once the base is destroyed. The Cylons plan to take humans hostage as protection, in case the humans renege, but agonise about doing so. Gaeta has his leg amputated. Baltar claims Roslin is sharing her visions with the Cylon Sharon and captive Six. Roslin is having visions of the Opera House again, and is stunned when Kara tells her the Hybrid talked of the Dying Leader and the Opera House. Roslin demands to talk to the Hybrid, and is taken to the Cylon ship, along with Baltar. Sharon/Athena is having the same dreams, of Six taking her daughter Hera from the opera House; Hera goes missing and Athena tracks her down, to the Cylon leader Six. Sharon shoots the Six. On the Cylon ship, Roslin orders the Hybrid to the plugged in: on awakening, she screams "Jump" ... and they do.
The shot Six dies; Adama has Athena confined to the brig. Raptors find a destroyed Cylon ship -- it looks like Roslin and the rest must be dead. Adama discovers the captive Six is pregnant, and confronts Tigh; they fight. Admiral Adama refuses to accept Vice President Tom Zarek as President, and refuses to stop the search for Roslin. He comes to realise that he has lost his objectivity, and hands command over, to Tigh. Lee Adama is sworn in as President. Admiral Adama waits alone in a Raptor for the search team to return, while the fleet jump to a new location.
As the Cylon ship jumps to the Hub, Roslin experiences visions of her own death. On the Hub, Deanna is resurrected, in order to bring unity. The ship arrives, and Helo and an Eight go to the Hub ship, and take Deanna. The Hub is then nuked -- now all Cylons are mortal. During the battle, Baltar is seriously injured. Roslin treats his injuries, but under the influence of morphine, he confesses to having given the Cylons the access codes that allowed them to annihilate humanity. She then decides to let him die, but during a further jump, she has another vision that convinces her to save him. Deanna arrives, and tells Roslin she is one of the five -- then laughs, saying it was a joke, and that she won't reveal the five until she gets back to the fleet. They continue to jump, and eventually reach Adama waiting for them. He and Roslin hug.
Deanna threatens to kill the hostages unless the four Cylons in the fleet are returned to her. Tigh confesses to the Admiral that he is one. Lee threatens to space the Cylons unless Deanna stands down. During the standoff, Starbuck discovers her Raptor now has a signal to Earth encoded in it. The two groups agree to cooperate and return the Earth. They get there, amid great rejoicing, but it is not what they expect...
[... mid-season hiatus due to writers' strike ...]
Earth is a radioactive wasteland, destroyed two thousand years ago. Everyone takes this badly. Roslin stops her medication and burns the book of prophesy. Dee shoots herself. Adama gets drunk and tries to get Tigh to kill him in a rage, but Tigh refuses. Only Apollo keeps relatively sane. Investigation reveals that the destroyed 13th tribe were in fact all Cylons. Down on the planet, the Four are having flashbacks to their lives their just before the destruction: how did they survive 2000 years? Meanwhile Starbuck traces the signal they have been following, until she finds her battered raptor, with her burned body inside it. She tells Leoben Conoy that the Cylon hybrid said she was the harbinger of death and would bring destruction to them all: he runs off in horror. Adama pulls himself together, addresses the fleet, and starts the search for another home. Down on the planet, Tigh walks out to sea, and has a flashback of him and his wife Ellen before the destruction: he decides she is the Fifth.
The general depression continues. Zarek starts angling for leadership, backed by an embittered Gaeta, while Roslin stops her medication. Tyrol discovers he is not the father of Cally's child. The allied Cylons offer to upgrade the fleet with their FTL drives, in return for citizenship and protection from the other Cylons. Outrage, mutiny, and politicking ensues.
Zarek and Gaeta stage a mutiny. Through a running firefight on Galactica, Lee and Starbuck rescue Roslin, who addresses the fleet using Baltar's illicit radio. They all escape in a Raptor, with Adama and Tigh staying behind to cover their escape. The mutineers throw a grenade into the hold...
... Adama and Tigh are captured. Roslin escapes to the Cylon base ship. Zarek brings the Council to Galactica, then has them shot; Gaetor is horrified. Gaetor insists Adama be put on trial for Desertion (on New Caprica) and Giving Comfort to the Enemy. Roslin persuades the Cylon ship not to jump away and desert the fleet. Starbuck and Lee break the captured Cylons, including Tigh, out of the brig, but Sam is mortally wounded in the escape; Starbuck stays with him. Adama is sentenced to death by firing squad, but is rescued by Tigh et al. Chief Tyrol disables the FTL drive, but notices damage to the hull. Adama retakes the ship, and Roslin returns. Gaetor and Zarek are executed by firing squad.
Sam with a bullet in his head remembers The Five, how they fled from Earth, and how they gave flesh and resurrection to the Cylons. Meanwhile, a resurrected Ellen is tormented by Cavil, who hates being a humanoid Cylon. When the Resurrection Hub is destroyed, he demands that Ellen gives them Resurrection again; she says she would need all Five, but he plans to cut her head open. Boomer helps her escape. The cracks in the ship worsen; Admiral Adama gives Tyrol permission to used Cylon technology to fix it. Roslin delegates the task of replacing the slaughtered representatives to Lee Adama. Sam undergoes surgery to remove the bullet before he can tell all his memories; the surgery is successful except that Sam is brain dead.
Boomer and Ellen return to Galactica. Tyrol starts the Cylon resin treatment on Galactica's bulkheads. The Five debate whether to return to the Cylon Base ship; Ellen plays mind games with Caprica. Gaius returns to his worshippers, who have been collecting food in his absence; he decides to distribute it to the hungry, but it gets stolen. He goes to Adama for guns to help him, and gets given them. Caprica Six loses the baby. Sam's brain activity restarts.
The Cylons demand that Boomer be handed over to them, to be tried for treason for siding with Cavil in the Cylon civil war, for which they will demand the death penalty. Roslin signs the agreement. Tyrol breaks her out of the brig, and puts her on a ship, not realising she has taken Hera. Starbuck hallucinates her father playing the piano in the bar, and recreates an old song her taught her, from the scribblings of Hera: it is the song the Five heard when they discovered who they were. Roslin collapses.
Boomer delivers Hera to Cavil. Sam is plugged into the datastream, and starts talking like a Cylon navigator, and affecting Galactica through the Cylon resin. Baltar outs Kara as "reborn". Adama decides to abandon Galactica.
Lots of flashbacks to New Caprica before the attack, showing Roslin, Baltar and Starbuck as they were before. Galactica is being decommissioned, and Adama sees a photo of Hera on the "lost" board. He gets Starbuck to ask Sam where the Cylon base colony is, and discovers it is near a black hole [well, actually, in "the accretion disc of a naked singularity", for the full technobabble]. Baltar demands Lee Adama give his followers a voice on the new council; Lee accuses him of being self-serving; he agrees that "I wouldn't trust me, either". Adama asks for volunteers to go on a "one way" rescue mission. He is joined by most of the core cast, including a very fragile Roslin.
The mission reaches the Cylon colony, and gets Hera. But Cavil and the Centurions raid Galactica. Roslin, Athena, Gaius and Caprica Six recreate their opera house dream chasing Hera, ending up on the Bridge. Cavil threatens to shoot Hera; Gaius suggests breaking the cycle. Tigh offers Resurrection in exchange for Hera; Cavil agrees, and calls off the fighters. The Five link to download the information, at which point Tyrol realises Tory killed Cally, breaks the link, and strangles her. All hell breaks loose again, and Adama orders Starbuck to jump the ship, anywhere. She remembers all the weird music stuff, and punches in a code based on that. They jump -- to Earth. Our Earth of 150,000 years ago, not their radioactive Earth. The fleet joins them. The flashbacks reveal each getting something like what they desired. The Gaius in Six's head, and the Six in Gaius' head, speak to them both, then disappear. Roslin dies. Kara vanishes. The rest spread over the planet and go back to basics.