New Caprica has been occupied by the Cylons for 4 months. Colonel Tigh has been imprisoned, but his wife trades to get him out. Starbuck is also captive, of Leoben Conoy, a Cylon obsessed with her [ 1.8 Flesh and Bone ] who wants to make her love him; she's already killed him six times. The Resistance is blowing things up, but of course the Cylons just download. The Cylons disagree how they should respond to the attacks. So they decide to go for a big target: President Baltar at the graduation ceremony of the new human-cylon police force. A suicide bomber strikes, but Baltar wasn't present. Meanwhile, in the fleet, Apollo has gone to seed, but Adama is determined to be ready to attack the Cylons. Finally, the Resistance get a signal through to the fleet...
Leoben Conoy introduces Starbuck to the daughter he says he made from her harvested ovaries. Initially hostile, she melts when the child has an accident. Adama commissions Sharon, and sends her down to New Caprica to make contact with the Resistance, but they are betrayed by Ellen Tigh, discovered, and Cylon robots open fire on them. The Resistance blow up the power plant. The Cylons decide to get tough, and arrest 300 humans, including Roslin, Zarek and Cally, and take them off to be shot, having forced Baltar to sign the execution order. One of the Caprica Police force frees Cally, but the Cylon robots open fire on the rest...
Sharon and the Insurgents escape the Cylon attack due to Sharon's Marine backup. Roslin and the others escape execution due to rescue by other Insurgents. Ellen Tigh's treachery is unveiled. The humans plan for escape from New Caprica.
Galactica comes to New Caprica, having sent Apollo and Pegasus off with the civilian fleet. The colonists are rescued. Pegasus returns, to rescue Galactica, and is destroyed in the process. Baltar discovers Sharon's baby Hera is still alive, and gives her to Three. Roslin reinstates herself in the Presidental suite. Starbuck discovers the child is not her daughter after all, but was stolen from a colonist by the Cylons.
Back on a crowded Galactica, Vice President Zarek is sworn in as President. He issues a secret Executive Order to allow "The Circle", six crewmembers including Tigh and Chief Tyrol, the power to try, convict, and execute collaborators. The Captain of the New Caprica police is spaced. Baltar is captive aboard a Cylon vessel, and the Cylons are voting on what to do with him. The Sixes get the casting vote. President Baltar's aide, Felix Gaeta, is condemned and nearly spaced, until The Circle realise he was the headquarters mole who allowed them to save all those on the death list. Zarek appoints Roslin as his Vice President, and resigns, leaving her President again (unelected, again!). She issues an amnesty for all collaborators.
Gaeta claims he can recreate some of Baltar's work on finding Earth -- it requires looking for a pair of red and blue pulsars. They go to investigate. Meanwhile, Baltar gives the same information to the Cylons to convince them to keep him alive. They also go to investigate, but the crew catch a disease deadly to Cylons. Baltar volunteers to investigate, finds an ancient probe, but doesn't tell the Cylons. Meanwhile, Tigh and Starbuck are getting drunk and fomenting dissent in the pilot's mess, about how the colonists suffered more than the fleet did, and how they know they did not become collaborators. Adama challenges them to shape up, or get out.
Galactica finds the infected Cylon ship, including some sick but still living Cylons, and realise they could use them to wipe out the Cylons. Humans are immune; Sharon is immune, because of her half-human baby. So they plan to take the infected prisoners within reach of a resurrection ship, and kill them, spreading the disease to all Cylons. Helo protests this would be genocide, and wrong, but is overruled. Sharon refuses to back him up. Roslin gives the go-ahead to use this biological weapon. But Helo kills the Cylons first. But not before they have revealed that Baltar is alive, on the Cylon ship.
Roslin discovers that Adama is about to achieve 45 years of service, so decides on a medal ceremony, to help boost morale. Then "Bulldog", a colleague of Adama's who was captured by the Cylons 3 years ago, escapes them and makes for Galactica. There he discovers that during the black ops covert mission inside Cylon territory that they were on, Adama shot him down rather than blow the mission. He tries to kill Adama. But Starbuck realises the Cylons let him escape, and confronts Tigh with the evidence. Tigh rescues Adama. Adama now believes he helped start the war, and offers his resignation to Roslin. She refuses, and makes him go through the medal ceremony as his penance.
Galactica has a boxing ring, allowing grudges to be brought out into the open, as opponents slug it out. Helo bashes Apollo, Adama fights the Chief, then Apollo and Starbuck slug it out. All through this, we see flashbacks to some of the incidents during the first days of settlement on New Caprica, including how (if not why) Apollo and Starbuck ended up married to other people.
The fleet has run out of food. Sharon finds a dangerous radioactive route through to a planet with algae suitable for food. The fleet starts the perilous mission of jumping there, accompanied by Raptors to give them coordinates. Starbuck discovers that ex-CAG Kat was a drug runner before the Cylon attack, and accuses her of not being able to change. Kat, accompanying one of the fleet ships, loses it for a moment, and knowingly stays to long in the radioactive field to find it again and bring it through safely. She dies of radiation poisoning. Starbuck feels guilty. Meanwhile, one of the Cylon Threes is constantly getting herself killed in order to experience what happens between that and download, but the images are too fragmentary to make sense. She and Baltar visit the hybrid Cylon pilot, who's bizarre ramblings give an obscure clue to look for "The Eye of Jupiter".
A team led by Apollo goes down from Galactica to the algae planet to harvest food. Down there, Chief Tyroll gets an urge to explore, and discovers an ancient temple. Four Cylon ships arrive, and ask to talk to Galactica. They say they want the Eye of Jupiter, which is down on the planet. The humans discover Baltar is still alive. Adama threatens to nuke the planet if they try to land. A Cylon ship did land when the Cylons first arrived, and they shoot down Starbuck. The team on the ground prepare to defend themselves from the Cylons. Sharon discovers her baby Hera is alive. They Cylons send six ships down towards the planet, and Adama arms his nukes...
The Cylons pull back five of their ships, and Adama disarms the nukes. The sixth ship has Baltar and Three on board, against the Cylon's wishes. Sharon begs Helo to kill her, so that she can download on the Cylon ship and rescue Hera. Apollo sends Dee off to rescue Starbuck. Sharon discovers that Hera is sick, and convinces Caprica Six to let her take the baby back to Galactica for treatment by a human doctor. The sun goes nova, the Cylons jump away, and the Chief realises it is the Eye of Jupiter, a road map pointing to an earlier nova. Three has a vision of the remaining five Cylons, and dies. Baltar is captured by The Chief. The Cylons tell the resurrected Three that they have decided to discontinue her line, and put her and all the other Threes in storage. Helo realises that the picture of the Eye from the temple is the same as a painting Starbuck did back on Caprica.
Roslin and Adama try to get Baltar to talk: to confess his guilt, and to tell them what he told the Cylons about the route to Earth. But he sees himself as a victim, not a criminal, so won't confess. Gaeta tries to kill him. Apollo and Dee, and Starbuck and Sam, get back together.
Due to overcrowding, some civilians are moved to Galactica. Helo is in charge of the operation. This includes a group of Sagittarons, who eschew medical intervention, but turn out to be sick. When one of the Sagittarons, Mrs King, tells Helo that she took her son to Doctor Robert to save him, but he died anyway, Helo gets suspicious. He discovers that the Caprican doctor, a hero of the Resistance on New Caprica, is deliberately killing the Sagittarons, and was down on New Caprica too. Adama, Tigh, and Dr Cottle don't want to believe him, but eventually realise he is right, and arrest Dr Robert. Meanwhile Zarek warns Roslin there will be chaos if Baltar gets a trial.
It's Adama's wedding anniversary, and his ex-wife comes back to haunt his memories. The Chief and Cally are trapped in a hanger with the air leaking out, and a desperate rescue mission has to be launched. Roslin asks Adama to ask Lee to chair the legal committee preparing for Baltar's trial.
A Viper crashes because of contaminated fuel; the workers on the refinery ship are exhausted and agitating for concessions; Roslin has the leader arrested when he quotes from Baltar's illegal book that he's smuggling out of his prison cell, charging the administration with producing an inherited officer class and working class. Chief Tyrol is put in charge of getting the refinery running again. He does, but is appalled at the conditions, and the number of children working there, and manages to get some extra hands to help. But when a boy loses an arm in the unmaintained machinery, Tyrol calls a strike. Back on Galactica, the deck crew also strike, and Tyrol is arrested. Adama charges him with mutiny, and threatens to shoot the mutineers, starting with ringleader Cally Tyrol. Tyrol backs down and calls off the strike; Adama sends him to talk to the President, who encourages him to set up a Union like he did on New Caprica. A deckhand is promoted and sent on Viper pilot training.
Out patrolling while the fleet is refuelling, Starbuck spies and pursues an enemy ship. But no-one else has any evidence of it. Apollo refuses to ground Starbuck, but she is having constant nightmares of the Eye of Jupiter mandala and Leoben Conoy, and is having visions of herself as a young child, and is beginning to doubt herself. She consults an Oracle, who tells her of her destiny. Apollo persuades her to fly again. She pursues another enemy craft, and is knocked out. She has another vision, of the death of her mother, who she had walked out on six years earlier. The being who looks like Leoben Conoy in her visions says that she is now prepared for her next trial, "between life and death". She regains consciousness, in a damaged Viper hurtling towards the planetary surface. Starbuck doesn't eject, and Apollo watchers her ship explode.
Baltar's defence lawyer is assassinated. Apollo is having difficulty coming to terms with Starbuck's death. Adama takes him off CAG duty, and puts him in charge of the security of Baltar's new defence lawyer, Romo Lampkin. After watching him in action, and talking to him after a nearly successful assassination attempt, Apollo decides he wants to help Lampkin.
Baltar's trial starts. Tigh is drunk during cross examination, and admits he killed his wife. Adama accuses Apollo of telling Lampkin about Tigh's wife. Apollo denies it, and resigns his commission when he is not believed. He cross examines Roslin, who admits that she is back on the hallucinogenic cancer drug, because her cancer has returned. Lots of people seem to be having some kind of musical hallucination.
Felix Gaeta lies about Baltar signing the death list without coercion. Lee Adama makes an impassioned speech about betrayal, justice and forgiveness from the witness box. Baltar is found not guilty of treason on New Caprica, to Roslin's dismay and fury. Roslin, Athena, and Caprica Six all have a simultaneous hallucination about Hera. The fleet jump to the nebula. There is a strange fleet-wide powercut, during which Roslin feels faint, and Tyrol, Tigh, Sam Anders and Tory Foster discover that they have been hearing music because they are Cylons. Baltar is hustled away by a secret group. When the power comes back, the fleet is under attack by a massive Cylon force. All the new Cylons report for duty. Apollo also reports for duty, and flies a raptor -- where he sees Starbuck, who says she has found Earth, and can lead them all to it...