There's a party on Galactica's flight deck as Flat-Top just had his thousandth landing. Something goes terribly wrong however when a drone accidentally goes off and explodes in a group of pilots. 13 are dead. During the ceremony Kara Thrace starts thinking about her dead fiancée Zak Adama. And those memories even get clearer when Adama orders her to start training new pilots. She seems very uncomfortable in doing so. The favor she did for Zak by letting him pass basic flight seems to bother her more and more. Angrily she stops training pilots after just one day. Meanwhile on Cylon-occupied Caprica Helo and Cylon-Sharon find a bomb shelter in a restaurant. It seems like a good place to stay for a while. There's food, water and anti-radiation medication in abundance.

Starbuck has been shot down over a barren moon, and must be rescued before she runs out of oxygen. Adama become obsessed with trying to save her even when all hope seems lost, putting the fleet at risk. Meanwhile, Starbuck finds the Cylon Raider she shot down, and tries to learn how to fly it so she can escape.

A humanoid Cylon straps himself with explosives and commits a suicide bombing in a crowded hallway on Galactica. Roslin and Adama are forced to publicly reveal that the Cylons now have models that look like humans, and a wave of paranoia spreads over the fleet as everyone starts being suspected of being a Cylon.

After Baltar has an argument with the vision of Number Six he sees in his head, a physical copy of Cylon model Number Six shows up in Galactica's CIC claiming to be a woman named Shelley Godfrey who has evidence that proves that Baltar has betrayed humanity...except that she's trying to frame him for an act of pre-attack sabotage.

Galactica stumbles upon Kobol, the long-lost home world of humanity that the 13 Tribes came from, which legend says holds the only clues to the location of Earth. Roslin convinces Starbuck to steal the captured Cylon raider and return to Cylon-occupied Caprica with it to retrieve a religious artifact that will unlock the secrets on Kobol.

Tigh has problems with the responsibility of being a leader, president Roslin loses control without chamalla. The Kobol team discovers a Cylon battery.

Tigh's decision to impose martial law is protested in the fleet as well as on Galactica. On Caprica, Helo and Starbuck meet other humans.

While Commander Adama tries to join Roslin's team on Kobol, Dr. Baltar's Number Six tells him he's crazy.

Journalist D'Anna Biers is making an item on the Gideon incident, when she's asked by Adama and Roslin to film daily life on Galactica.

While Tyrol decides to start building a new fighter, the Cylon virus is rearing its ugly head again. Boomer says it means a large Cylon attack is imminent.

Adama and Cain find common ground when Starbuck returns with footage of the Cylon ship. Roslin negotiates a temporary truce, while Starbuck plans an attack.

President Roslin, who is about to die, believes Sharon's baby is dangerous and orders it must die. Meanwhile, a terrorist group inside the fleet starts to ask for a peace negotiation with the cylons.

Apollo investigates the murder of one of the crew and falls for a young prostitute, whom he vows to save from the rogue ship dealing with the Black Market. As well as confronting the bad guys, Apollo has to confront some past mistakes.

Two of Pegasus' raptors go missing after a suspicious distress call. President Roslin must make a decision on abortion that could hurt her political career.

The Cylon baby is finally born, leading to some political decisions being made. Meanwhile, the Cylons on Caprica contemplate life and humans when they meet up with a certain human from a previous episode. This story explores the Cylon world.

The group on Caprica is under fire by the Cylons, but suddenly they stop. With only one ship's votes to be counted, Roslin is way behind in the elections.

The secret source in the administration has provided Tyrol with a list of all humans scheduled for extermination. Tyrol's wife Cally is on the list and he sets off to rescue her. Sharon Agathon has made it safely to the planet but they are ambushed by Cylons lying in wait. They realize they were betrayed and Anders finds damning evidence that points to the identity of the traitor. D'Anna Biers has been having strange dreams of late and an oracle tells her that the child Hera is alive and she will hold her in her arms. Roslin meanwhile assigns a squad of men to protect the child at all costs. The Admiral sends the Pegasus away with the few remaining civilian ships to continue the search for Earth.

When a group of ill Cylons from the infected Basestar is brought to Galactica, Lee discovers a way to solve the Cylon problem forever - by destroying the whole Cylon race. Meanwhile, D'anna's acts to discover if Baltar is reliable will forge an unusual relationship.

A figure from Adama's past returns to haunt him. His return raises questions about why the Cylons launched their initial attack against the Twelve Colonies.

A look at the events that took place during the year-long gap from the storyline in the Season Two finale. The story reveals the reasons for the rift between Kara ("Starbuck") and Lee ("Apollo").

The Colonial fleet makes a harrowing journey. Kat plays a vital role in the success or failure of the passage.

Baltar plays a game of cat and mouse with Adama and the President, thinking they will kill him once they've gotten out of him what they want to know. Lee deals with his feelings for Kara, while struggling to hang on to his marriage.

When a group of refugees board Galactica with a curable illness, it becomes very mysterious when they begin to die after taking the injection they do not believe in.

Coincidences creates new alliances aboard Galactica.

The aftermath of a coup among the Cylons leads to further violence, Lee finds himself facing off against Roslin during his first meeting with the Quorum of Twelve as the new representative of Caprica, and Cally discovers the horrible truth about her husband Galen Tyrol. Meanwhile, Starbuck aimlessly searches for Earth with Anders and other Galactica officers.

A vicious injury ends the mutiny attempt aboard the Demetrius, Kara leads her crew to the Cylon rebel's Basestar, and Roslin begins to understand Gaius Baltar's appeal to his followers. Meanwhile, Anders attempts to secretly find answers to his purpose as a member of the Final Five.

A shaky alliance between the Colonial Fleet and Cylon rebels is put to the test when the two groups combine efforts to take out a Cylon "Resurrection Hub". Meanwhile, Athena loses control when Hera becomes unnaturally drawn to Natalie.

President Roslin's abduction by the Cylon Hybrid triggers a bitter power struggle within the Colonial Fleet.

The Hybrid keeps jumping the basestar, and Roslin has visions. The three, D'Anna, is un-boxed. Humans and Cylons engage in a battle to destroy the Resurrection Hub. Baltar is badly wounded and Roslin has to decide whether or not to help him.

Adama considers Saul and Tyrol's suggestion that the Fleet should integrate Cylon jump technology since it will triple the distance they will be able to cover before they run out of fuel. But the Cylon's condition is that they will be allowed to join the Fleet, for safety against Cavil, who's still out there. Ultimately, the decision is up to President Roslin, but Zarek calls the Quorum and gets them to carry the motion that no Cylon be allowed aboard any Colonial vessel unless permitted by the ship's captain. Tyrol learns from Dr. Cottle that Cally had their child tested and the results indicated that Tyrol is not the father - therefore the child is fully human. Roslin starts her climb up from the depths of despair she had fallen to soon after the Fleet found Earth.

Eighteen months ago: Saul poisons Ellen, who then finds herself downloaded into a new body aboard a Cylon Base Star, with a single Centaurion keeping watch over her. After the initial shock, she has a revelation as she remembers things she had forgotten. Present Day: Dr. Cottle is operating on Anders, who has a bullet lodged in his brain. Anders starts to remember things he had forgotten. Eighteen months ago: Cavil comes to see Ellen, who calls him John, because that's his "real" name. Cavil says he hates that name. John was the first Cylon model *Ellen* created. She also created seven others. So, there are actually only *eight* Cylon models and the "Final Five" are actually copies of humans who lived 2,000 years earlier and, together, created Resurrection, which allowed them and the Cylons to download. Number Seven, Daniel, was a favorite of Ellen. Jealous, John sabotaged the process of using Resurrection on Daniel, making him unique. John and Ellen start a months-long philosophical and ethical argument on Cylon - human interaction. John says he started the genocide of humankind because his "forebears on the Centaurion side of the family were the slaves of humanity." And he wants justice for that. Present Day: Anders tells Starbuck that he has seen "everything" and needs Kara to get "the others" - Galen, Tory, Saul and Ellen to his bedside. Anders says he remembers everything and knows why they have come all the way to Earth... Adama reinstates Tyrol as a Chief of Engineering. Tyrol starts inspecting the damage Galactica has taken during their journey. But he is not prepared for what he finds and Adama is not prepared for what Tyrol suggests as a repair method.

Ellen and Boomer travel to the Galactica. Saul is entranced at the sight of his wife while Adama puts Boomer in the brig. Ellen is not so pleased when she learns that Caprica Six is pregnant by Saul. Her interference and jealousy leads Six to have a miscarriage. Sam Anders survived the operation but now seems to be brain dead. Ellen is disappointed that the Final Five cannot be completely reunited. By majority vote, the Five agree that they will go off on their own, leaving the Colonial Fleet behind. Adama has agreed to have the cracks in the Galactica's hull repaired using a Cylon living resin.

Kara meets a pianist who reminds her of her father. She tries to play a melody she remembers from her childhood, and a drawing made by Hera helps her. Meanwhile, Boomer is to be tried for treason. Tyrol takes her side, and helps her escape.

With Hera now likely in the hands of John Cavil, Admiral Adama sends out search teams to locate The Colony, the Cylon home world if you will, that Ellen Tigh says is the only place she imagines she could be. Adama reluctantly comes to the conclusion that the Galactica has reached the end of its days. He orders all repair activities halted and decides to strip the ship and share everything that is salvageable with the rest of the fleet. Starbuck meanwhile shares with Gaius Baltar what she found on the uninhabitable Earth. He subsequently - and quite publicly - proclaims her to be an angel.

The Colony is located sitting on the edge of a black hole with only one point of entry in what is a very large debris field. Knowing that the Galactica has reached the end of the line, Admiral Adama asks for volunteers to mount a raid on the Cylon base, realizing it may be the ship's last jump. In flashbacks prior to the Cylon invasion, key moments in the lives of several of the crew are presented. These include include the first time Kara Thrace and Lee Adama meet; Admiral Adama's struggle with his decision to retire from the colonial fleet; Gaius Baltar's relationship with his father and his developing relationship with Caprica Six; and Sam Anders discussing the motivation behind his professional sports career.

A stripped down Galactica attacks the Cylon's Colony ship in the hopes of rescuing Hera. The meaning of the shared dream in the Opera House on Kobol is revealed. Sam Anders is moved in his Hybrid tank to the CIC in the hopes that he will be able to assist the combatants. Their mission complete, Admiral Adama orders Starbuck to pick a destination - any destination - to which the ship can jump to get out of there. With that, the meaning of the tune and the musical notes are explained. Having successfully jumped, the old Galactica has truly reached the end of it's life. A planet capable of sustaining life is found and Lee Adama makes a radical proposal for the future of humankind. In a flash forward far into the future, Hera's importance to the human race is revealed.

As conflicts reach a climax, Cylons and humans face a stark choice.