In the wake of the Cylon sneak attack, the ragtag fleet of human survivors is forced to play a deadly game of cat-and-mouse with their pursuers. Every 33 minutes, they make a jump to a new location. And every 33 minutes, the Cylons manage to find them. The pilots are on the brink of exhaustion, relying on artificial stimulants to keep fighting, and the civilians are beginning to doubt the leadership of Commander Adama and President Roslin.

Lt. Sharon Valerii wakes up soaking wet in the tool room with an explosive charge in her duffel bag. Shortly afterward, a mysterious explosion destroys all the port-side water tanks on Galactica, creating a crisis for the entire fleet. Sharon can't remember a thing, but all the evidence points to her as a saboteur. She confesses her concern to Chief Tyrol, but he can't believe she's responsible.

 The fleet has found a source of water, but who will take on the difficult and dangerous job of mining it from the icy planet? Commander Adama and President Roslin send Lee to the Astral Queen, a prisoner transport ship, with an offer for its inmates: Volunteer for this mission and earn "freedom points."

After a flight deck accident kills 13 pilots and wounds many others, Kara is thrust into service as a flight instructor and ordered to turn a group of civilian pilots and academy washouts into full-fledged Viper pilots.
The assignment brings back painful memories for Kara. She can't forget how she let Zak — Commander Adama's son and her lover — pass Basic Flight when he wasn't ready, and how it ultimately cost him his life. Determined never to repeat the mistake, she flunks out the would-be pilots on their first day.

 When Lt. Kara Thrace goes missing in action after encountering a Cylon patrol while on a training mission, Commander Adama feels responsible — especially in light of her recent admission that she blames herself for his son Zak's death.
Both Adama and Lee devote the full resources of the fleet to search for their missing fighter ace, causing some to wonder if it's worth risking the lives of 45,000 people to save one downed pilot. When President Roslin questions their motives and points out that Kara's oxygen was exhausted hours ago, they reluctantly call off the search.

 When a new copy of Doral, a Cylon who had been previously exposed while serving as the Galactica's public-relations officer, sneaks aboard and blows himself up, killing three people, Commander Adama and President Roslin must finally make public the terrifying secret known only to a select few: Cylons now look like humans.
Adama also appoints an independent tribunal to investigate the recent security breaches and names Sgt. Hadrian as lead investigator. When Hadrian discovers a hatch was left open, even after Chief Tyrol had reported that all were closed, she focuses the investigation on him and his relationship with Sharon.

When Baltar and the Number Six who lives in his head have a falling out, she abandons him, only to surface a short while later aboard the Galactica. But now she's called Shelley Godfrey, everyone can see her, and she's telling them that she has evidence, passed on by the late Dr. Amarak, that will prove Baltar sold out the human race to the Cylons.

 A Cylon, who calls himself Leobon, is discovered on one of the ships in the fleet. Commander Adama sends Kara to interrogate him — or, rather, it. The Cylon tells Kara that he planted a nuclear device on one of the ships. Although she doesn't believe it, Kara passes on the warning.
As her colleagues search for the device, Kara engages Leobon in a battle of wills. Theological debates about souls and the humanity of Cylons lead to mind games, threats, and, ultimately, torture. Taking a personal interest in what Leobon has to say, President Roslin joins the interrogation.

President Roslin's fears that Commander Adama is a Cylon are stoked when she learns he's making secret wireless calls to other ships. Then, to make things worse, a single Cylon raider appears near the Galactica and begins acting strangely after being damaged in battle.
When Adama returns to the ship with Tigh's wife, Ellen, an earthy temptress and irrepressible flirt who claims to have been in a coma since their civilization was destroyed, Roslin's suspicions increase. She orders Baltar to screen both Ellen and Adama with his newly completed Cylon-detector.

As its fuel supply dwindles, the fleet must seek out a new supply of tylium ore or risk becoming sitting ducks to any Cylon attack. A recon patrol finds an asteroid full of the fuel, but there's a catch — the Cylons have found it first and established a heavily guarded refining plant.
Kara devises a plan: Jump three decoy ships near the asteroid; when the Cylons attack, destroy their bases, leaving them stranded in space. It's a bold tactic, but it will take luck, skill and daring to pull it off.

 When President Roslin calls an Interim Quorum of the Twelve Colonies, she discovers that democracy brings its ugly stepsisters — politics and deadly intrigue — to the party. Tom Zarek, the charismatic convicted terrorist, is elected as the delegate from Sagittaron and immediately proposes elections for the vice-presidency.

 Roslin encourages her trusted adviser, Wallace Gray, to run against Zarek, but when he proves less than popular, she turns to the suddenly popular Baltar as her candidate.

While flying a supply patrol, Crashdown and Sharon Valerii discover a bountiful planet that can support human life. Indeed, it might be Kobol, the legendary "home of the gods." The discovery prompts Commander Adama to send a ground team to investigate; it also gives new life to President Roslin's belief that she is a tool of destiny and that this discovery, like her rapidly spreading cancer, is part of an ancient prophecy.

The Galactica and her crew discover Kobol the mythical homeworld of humanity - Cylon raiders take out a Raptor over the planet - Baltar discovers more about his true destiny.
The fighters challenge the Cylon ship and Roslin is determined to find a way of reaching Earth. Last in series