Forty years after the end of the Cylon War, the artificially-created Cylons declare war on humanity by attacking and destroying the twelve colonies. The military crumbles after their newly updated ships shut down in the face of a new unknown Cylon weapon. A lone battlestar known as Galactica, due to be decommissioned and converted into a museum, turns out to be the only thing standing between the Cylons and the total destruction of the human race.
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.
With water now found on a nearby moon in the form of ice, a labour source must be used to mine it. The answer is to use the prisoners aboard the Astral Queen. However, convicted terrorist Tom Zarek acts as their leader and organises a revolt, taking hostages with the demand of President Roslin's resignation.
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.
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.
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.
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.
When a Cylon agent is found aboard a ship in the fleet, Adama, by Roslin's request, sends Kara to interrogate the one called Leoben Conoy. Though she approaches impenetrable to his tactics, the Cylon engages her in a discussion of his specific dogma, including how special he believes Kara to be.
With Baltar's Cylon detector now operational, Roslin wants Adama to be the one to go first. Adama himself has been acting odd lately, due to his discovery of Tigh's wife, Ellen. The tackling of suspicion between the President, Commander, Colonel and his wife puts Baltar in the middle with the painstaking chore of the screening process.
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.
President Roslin uses the arrival of Colonial Day to form a new Quorum of Twelve. But soon Sagittaron's elected delegate Tom Zarek proposes that a vice president be chosen, his popularity quickly earning him a nomination. Not wanting to play into whatever Zarek maybe plotting, Roslin is adamant to choose her own 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.
By Roslin's request, Kara has jumped to Caprica to retrieve the Arrow of Apollo where she encounters a familiar face and a startling revelation.
Following Kara's defiance of his orders, Adama has more betrayals waiting for him - one coming from the most unexpected person.