Col Tigh is forced to assume the leadership duties on the Galactica fleet with Adama fighting a deadly bullet wound fired by cylon Sharon and President Roslin incarcerated following her own struggle for power with Adama.
Tigh and Lee work together to try and stop a group of Cylons from boarding the Galactica and causing the destruction of the entire fleet.
While Adama is still undergoing surgery, the Kobol group are trying to stop a Cylon weapon from taking out their air fleet. Meanwhile, over on the Galactica, President Roslin is coming down from the effects of a medication, while Colonel Tigh declares a state of martial law to silence his detractors.
With martial law in effect, the fleet ships are refusing to refuel the Galactica. Col Tigh has Chief Tryol put in the brig on suspicion of being a Cylon, and only Baltar can help exonerate him from the charges. Adama helps President Roslin get out of her cell and the two find a hiding spot on Cloud 9. Meanwhile, on Caprica, Helo and Starbuck encounter a group of survivors.
Commander Adama returns to take command of his ship before an ecstatic crew and corrals a search party for President Roslin. Shortly thereafter, President Roslin manages to send out a message telling of Earth's whereabouts and a plan to lead the fleet in its direction. Meanwhile, Starbuck recovers from a gunshot wound on Caprica and enlists Helo to help investigate the hospital facility in which she is housed.
The coalition of President Roslin is severely tested, while Adama reels from his son's betrayal. Meanwhile, Starbuck, Boomer and Helo head out to Athena after making their way back from Caprica.
Adama goes to Kobol to retrieve President Roslin and reconvene the Galactica fleet.
A reporter and her cameraman come aboard the Galactica to get a story on the conditions of living that exist during a war.
Adama learns that the Galactica and all its functions are being manipulated from the inside by a computer virus, with an impending Cylon attack on the way. He tries to decide whether or not he will safely be able to trust the ship to assist them in battle. Meanwhile, a new fighter ship is being designed by the flight team.
The Battlestar Galactica learns that the Battlestar Pegasus was the one other ship that managed to make it through the Cylon attack.
The Battlestar Galactica fleet and Pegasus go head to head with a Resurrection ship. Meanwhile, the ships' humans engage in a power struggle amongst themselves, threatening their very unity.
The Galactica fleet and Pegasus attempt to stand their ground against the powerful Cylon Resurrection ship in battle.
President Roslin lies dying and flashes back to her young life on Caprica. Meanwhile, a radical bunch of Cylon supporters create havoc in order to facilitate an immediate Cylon peace.
President Roslin tries to stop the practice of black market trading, which prompts upheaval and an investigation which leads into as far up as the highest levels of government branches.
The Galactica Viper pilots must help protect a Colonial mining area which is being bombarded by a Cylon raider.
Adama is ordered to hand over Sharon by a woman who has decided to create a hostage situation on Cloud Nine as retribution for her husband's murder by Cylons.
Adama and the new captain of the Pegasus forge an uneasy relationship when they try to find a team of Raptor scouts that vanished.
The order of the Cylons is unveiled after a dead Cylon's awareness is downloaded into a different body.
A chance at peace between humans and Cylons arises, but the Cylons have some severe demands, hoping to force the humans into accepting the Cylon religion and allowing the Cylons to use some humans for breeding purposes. When the fleet begins to side with the Cylon idea of forging peace, a skeptical President Roslin must try and use her authority to keep this plan she doesn't believe in from becoming a reality.
President Roslin is forced to decide whether or not she will rig the election or step aside and let Baltar win.