... Adama has been critically injured by Boomer; a shuttle team is down on Kobol under attack; Roslin and Apollo are in the brig; Tigh is in command. The fleet has to jump because Cylons appear, possibly guided to their location by Cylon Boomer. Galactica ends up separated from the rest of the fleet because of a navigational mix-up -- and there is no doctor on board to perform emergency surgery on Adama. On Kobol, Six shows Gaius a vision of their future baby. Meanwhile, on Caprica, while Helo argues with Starbuck about killing Boomer, Boomer steals Starbuck's spacecraft, stranding them. [Remember: always lock your vehicle, even when you think there is no threat.] After dangerously networking their computers together to perform the needed navigation, Galactica rejoins the fleet, but has been boarded by a Cylons... [So, they can monitor the Cylon viruses successively penetrating their multiple firewalls, but not stop them. And what about the progress of those viruses they couldn't detect...]
The Cylons rampage through Galactica, attempting to vent the atmosphere, and gain control of the guns to take out the rest of the fleet. Viruses have taken down a lot of the power, so it's a lot of running about in dark corridors. Apollo saves the day, but Tigh is not impressed. On Kobol, the members of the shuttle team are dying one by one, and Gaius has a vision of Adama drowning his baby. On Caprica, Starbuck and Helo visit her old apartment, and get some ground transport.
The downed shuttle crew on Kobol realise that the Cylons are building a missile battery to attack any rescue mission. The Lieutenant conceives a suicidal plan to destroy the battery, but Cally freezes in panic. He threatens to shoot her, but Gaius shoots him in the back first, winning Six's approval. Chief Tyrol then leads an attack on the guidance radar, destroying it as the rescue team arrives. The Twelve demand to see the President, but Tigh keeps them isolated. Roslin is very sick due to the withdrawal of her medication, and Ellen Tigh tells Colonel Tigh to let the Twelve see her in that state. But Roslin's guard has got her some medication, and she convinces the Twelve that she is the prophesied dying Chosen Leader. Tigh declares martial law.
Tigh throws Chief Tyrol in the brig with Boomer, on suspicion of being a Cylon. Gaius, while pretending to test Tyrol for Cylon-ness, threatens to kill Tyrol unless Boomer tells him how many other Cylons are on board -- she tells him there are eight. Apollo and President Roslin escape Galactica to set up a resistance. Specialist Cally shoots and kills Boomer. On Caprica, Starbuck and Helo meet up with the Resistance.
Starbuck is shot during an ambush, and captured by the Cylons. They treat her wound, and she discovers she is about to become part of a Cylon breeding farm. Roslin plays the religion card, and persuades 24 fleet ships to follow her to Kobol to find the Arrow of Apollo, and the route to Earth. Sharon tells Helo where Starbuck is being held, and helps rescue her. Starbuck leaves Caprica with the Arrow of Apollo.
Starbuck arrives at Kobol with the Arrow. Roslin orders Sharon thrown out of the airlock, but Sharon tells her she knows where the Tomb of Apollo can be found. Zarek and his sidekick plot against Lee. They all go down to Kobol to follow the path, and are attacked by Cylons, killing the Gemini member of the Twelve. Sharon saves the rest of them. Meanwhile, Adama, after some bad decisions, decides to go to Kobol to reunite the fleet.
Zarek's sidekick tells Sharon the others will kill her. Adama joins the searchers on Kobol. Sharon learns what happened to the other Boomer on Galactica, and agrees to kill Adama once they reach the tomb. But she flushes out the sidekick's plot, and kills him instead, and gives herself up to Adama. Inside the tomb of Athena, Adama, Roslin, Starbuck and Apollo are transported to Earth, where they see the sky map of the constellations of the Twelve tribes. Six tells Gaius she's not a chip in his head, and that he's mad. He gets a brainscan: no chip. But then he learns something that Six once told him -- so she can't just be an hallucination. A reinstated President Roslin is welcomed back to the fleet.
A reporter [Lucy Lawless] is threatening to inflame opinion about the "Gideon Massacre" -- which occurred when Tigh sent the Marines in to secure supplies. So Roslin and Adama give her "free access" to Galactica, to produce a documentary about what life is really like. She films Sharon in sickbay -- having some trouble with her pregnancy. However, she is brought round to seeing the crew as deserving support, and does not include that clip. The final documentary shows the heroism, and warts, of the Galactica crew. The Cylons pick up a copy of the documentary -- including the deleted clip of Sharon, and are delighted that she is still alive, and pregnant.
A Cylon virus has infected Galactica, threatening to overrun systems and use the ship as a weapon against the rest of the fleet. Sharon says this is a prelude to an all-out attack. She helps Galactica, by relaying a virus back to the attacking Cylon fleet, allowing them to be destroyed. Roslin discovers she has less than a month left to live. The chief decides to build a replacement Viper, and gradually gets everyone involved in the project. The crew name it Laura , after the President.
Battlestar Pegasus discovers the fleet -- and Admiral Helena Cain assumes command. She reassigns Apollo and Starbuck to Pegasus, and puts her own deck chief in charge over Tyrol. She and Adama plan an attack on a Cylon fleet, and send out a reconnaissance mission. Starbuck is left out of the mission, but takes the stealth fighter to gather intelligence. Gaius discovers a badly abused Cylon prisoner on Pegasus: it's a Six, and his own internal Six is very distressed by the discovery. Some of the Pegasus crew joke about how they've been abusing their own Cylon, and that they will do the same to the one on Galactica. Tyrol and Helo charge down to the brig, and discover the Pegasus interrogator raping Sharon. In the ensuing fight, he is killed. Cain takes them both back to Pegasus, and sentences them to death. Adama launches a marine strike force to retrieve them, and Cain launches her own raiders against Galactica...
... the mutual attack is halted by Starbuck's return reconnaissance mission, with detailed pictures of a giant Cylon ship. The Pegasus captive Six identifies it as the Cylon "Resurrection" ship, containing clone bodies for Cylons to download into. A temporary truce is called while the fleet plots how to attack the Cylons, but a dying Roslin warns Adama that he will have to kill Cain. Cain promotes Starbuck to CAG, and tells her that it's her priority to rescue the survivors on Caprica. Cain's number one tells Tigh how Cain stripped her own civilian fleet of spares and people, and shot the families of those who refused to cooperate. Adama orders Starbuck to kill Cain after the attack. Meanwhile Cain plots to kill Adama ...
... the attack is successful, and the Cylon Resurrection ship is destroyed. Apollo is adrift in space after having to eject from a damaged Blackbird, but is rescued just in time. neither Adama nor Cain give the order for the other to be assassinated. Gaius helps the captive Cylon Six clone escape. She wants him to kill her, but he gives her the gun and tells her to seek justice. She kills Cain. Roslin promotes Adama, now in command of two Battlestars, to Admiral.
Roslin lies dying, having flashbacks to just before the Cylon attack, when she averted a dangerous teachers' strike, to the fury of the President. In those flashbacks, she also saw Gaius and Six. Meanwhile, Cylon sympathisers who want to sue for peace are causing sabotage. Pegasus-Six is one of their leaders, but they don't know she is a Cylon. Roslin's doctor discovers an anomaly in Sharon's baby's blood, and Roslin orders it aborted. Head-Six demands that Gaius use his powers as president-to-be to save the baby, and Pegasus-Six that he use the power to surrender to the Cylons. But Gaius refuses, and realises something about the fetus's blood, and uses it to cure Roslin's cancer without aborting the baby. But he later reads the letter that Roslin wrote him when she thought he would be President, and realises that she will never trust him. Roslin agrees to talk to the sympathisers -- but Gaius sends them a nuclear bomb.
The recovered President Roslin decides that the rampant Black Market in the fleet must be shut down. The the commander of the Pegasus is murdered by Black Marketeers. Apollo is tasked with tracking down the killers. But everyone is implicated, right up to the Vice President. Apollo kills the Black Marketeer's leader, but lets the market itself survive, since it is essential to the fleet's operations. Roslin asks Gaius to quit as VP, but he refuses.
The Cylons have stopped attacking en mass: now that their Resurrection Ship is destroyed, they can't afford the casualties. Galactica and the Vipers are defending a mining ship, being slowly picked off by a Cylon raider known as "Scar". Starbuck goes up against him, but realises that her edge has been blunted, because she now has something to live for: or rather some one , back on Caprica.
A group who have learned there is a Cylon agent on Galactica take a crown hostage on Cloud 9, demanding the Cylon be handed over to them. The hostages include Ellen Tigh, Apollo, and Billy. Starbuck is smuggled in as an atmosphere technician, but her cover is blown, and in the ensuing gun battle, she accidentally shoots Apollo, badly injuring him. Adama agrees to send them Sharon, but dead. They realise that they have been tricked by an old corpse when the Marines burst in. In the ensuing gun battle, Billy is killed.
Apollo is sent to Pegasus to sort out problems between her new "by the book" Commander and Starbuck. While there a Raptor goes missing, and a distress call is heard. Despite orders to investigate cautiously incase it is a Cylon trap, the Commander jumps to rescue his crew. It is a Cylon trap. In the ensuing battle the Commander is killed. Adama promotes Apollo to Pegasus Commander. [Given that many problems have been caused by Adama putting the wrong person in charge, this might be interesting.] Meanwhile, a young woman is found stowing away to Galactica, for an abortion. The Geminis demand her back: abortion is not allowed in their religion. Roslin has always been a right-to-choose advocate, and refuses, even when they threaten to withdraw their support for her in the up-coming Presidential elections. But then Gauis tells her that at current replacement rates, humanity will be extinct in 18 years, so she very reluctantly issues a Presidential decree outlawing abortion. Gaius then publicly denounces this loss of freedom, and states that he plans to stand for President.
On Cylon-run Caprica, the downloaded Six who seduced Gaius is having problems -- she's a celebrity war-hero to the other Cylons, but has her own Gaius in her head, berating her. Then she is introduced to the downloaded-Boomer (killed on Galactica after shooting Adama), who is having even more problems adjusting to being a Cylon. Then Boomer tells Caprica-Six that Gaius survived the bombings, and is on Galactica. Together they decide to form a "Cylon resistance", preaching that vengeance against the humans is wrong. meanwhile of Galactica Sharon's baby is born prematurely. Roslin arranges for it to be secretly adopted, so that all the Cylons in the fleet believe it to be dead: Sharon is distraught, as is Six-in-Gaius'-head.
Chief Tyrol is woken from a nightmare by Cally, and attacks her. Starbuck gets permission to take a Raptor squadron to Caprica to rescue the survivors, navigated by Sharon. Roslin is ahead in the polls, until one of the raptors gets lost and discovers a planet, which Gaius declares to be New Caprica, a potential home... Starbuck finds the small group of survivors, and they all come under attack by Cylons...
... the Cylons inexplicably pull back, and everyone gets back. One of the returnees is a Cylon and delivers a message: the Caprica hero Cylons have persuaded the rest that their vendetta against the humans is wrong, so they are withdrawing. Roslin is losing the election due to the issue of New Caprica, and authorises electoral fraud. But it is discovered, and Adama persuades her to concede. Gaius is President, and issues a decree to colonise New Caprica. The Six freed from Pegasus sets off the nuclear bomb that Gaius gave her. ... A year later, most people are living in shanty squalor on New Caprica, with hardly any personnel left in the fleet. Gaius is a dissolute President as all falls to pieces around him. Roslin is back to being a schoolteacher. Then a Cylon fleet arrives, having detected the residue of the nuclear explosion a light year away. The remnants of the Galactica fleet jump away. The Cylons land, led by the Caprica hero Six and Sharon. They say they will not harm the humans if they do not resist. Gaius surrenders the landbound humans.