Colonel Tigh takes over the command of the Galactica due to Adama's critical injuries. A Cylon attack forces the fleet to make an emergency jump. A miscalculation causes the Galactica to be separated from the rest of the fleet.
On Kobol, Tyrol and Cally risk their lives to retrieve medicine for one of their wounded colleagues.
The Galactica successfully reunites with the fleet, but the Cylons are still onboard the ship. Col. Tigh orders Lee to stop the Centurions from reaching Aft Damage Control before they vent the atmosphere from the ship.
On Cylon-occupied Caprica, Starbuck and Helo visit her old apartment. Helo takes note of the abstract paintings on the wall.
On Kobol, Baltar has a nightmare about Adama. Tyrol and Cally go on a purported rescue mission.
Adama is still in surgery. Meanwhile, the men and women on Kobol are searching for a way out of their desperate situation. They discover that the Cylons have built an anti-aircraft battery, which is designed to destroy any rescue craft. Crashdown leads the group on a raid to destroy the weapon before their rescue ship can arrive.
Back on Galactica President Roslin is experiencing withdrawal symptoms after being deprived of chamalla. Colonel Tigh is facing off against the Quorum of Twelve. Fed up with their interference, he declares martial law.
Martial law is having a bad effect on the fleet as ships are refusing to resupply Galactica. The Chief is arrested as a suspected Cylon, and it's up to Gaius Baltar to prove his innocence. The President, with the assistance of Lee Adama, escapes her imprisonment aboard Galactica and takes refuge on Cloud 9 with the help of the most unlikely of allies.
Starbuck and Helo discover a group of fifty-three survivors on Caprica.
A week after last week's exciting episode , Adama returns to an excited CIC and retakes command of his ship. He orders a ship to ship search to find the President, but fails to find her before she sends out a message informing the other ships in the fleet that she knows where Earth is, and that she will lead them there. Over a third of the fleet leaves Galactica's protection and jumps back to Kobol to await the return of Starbuck.
Back on Caprica Starbuck has been shot and is under medical care in a strange looking and sounding hospital.
Caprica Boomer returns to Helo, and helps him lead a raid on the hospital where Starbuck is being held which leads to a chilling discovery.
President Roslin's fragile coalition is put to the test and Adama continues to struggle with the betrayal of his son. Starbuck, Helo, and Boomer return from Caprica and set out for Kobol to find the tomb of Athena.
Adama heads to Kobol to find Roslin, reassembles the fleet and heads down to Kobol himself with most of the key characters (Apollo, Starbuck, Zarek, Billy, Tyrol) to find the presidential party in search of the "tomb of Athena" which allegedly leads to Earth.
The two groups meet, Adama and Roslin make their peace and continue on their expedition. Apollo hangs out with Starbuck , Zarek tries to keep his cronie off plotting with Boomer who is unaware of tension building between Helo and Tyrol.
On arrival at the tomb, a showdown between Boomer, Adama (and Zarek's chum) occurs but the key characters of the group enter the tomb afterwards and find themselves transported to Earth.
A reporter is sent to Galactica to chronicle the harsh realities of life during wartime. Lucy Lawless guest stars as the television reporter, D'Anna Biers.
Sharon informs Adama that the Galatica has been infected with a computer virus that is tampering with the basic ship functions and is scanning them for weaknesses. All this is preparation for a major assault by the Cylon Raiders. So with the clock ticking, Adama must pull himself together and decide whether or not she can be trusted. Meanwhile the flight crew is hard at work on a new fighter named The Blackbird.
The Galactica crew is overjoyed when they encounter another Colonial battlestar, the Mercury-class Pegasus. The elation fades when Admiral Cain takes command of the fleet.
The Galactica crew learn about the harsh practices onboard Pegasus. The tension boils over when Helo and Chief Tyrol learn about Lt. Thorne, the "Cylon Interrogator."
Kara arrives in the Blackbird with detailed photos of the mysterious Cylon ship. Despite the new truce between Adama and Cain, Roslin continues to see Admiral Cain as a dangerous threat, one that needs to be dealt with firmly.
The Galactica and Pegasus prepare for a joint attack on the Cylon Resurrection Ship.
Adama assigns Kara a dangerous special mission. Lee says he will help Kara, but he may not have the will to fight, even to save his own life.
Meanwhile, Cain assigns Col. Fisk to his own special mission onboard the Galactica.
As President Roslin nears death, Dr. Gaius Baltar must be groomed for the worst case scenario.
Roslin orders the death of Sharon's unborn child.
A sabotaged Viper leads to an investigation that uncovers a movement of people seeking peace with the Cylons.
Baltar discovers an anomaly in the (Sharon's) fetus that may cure Roslin's cancer.
The new commander of the Pegasus, Jack Fisk, is cuddled by black marketeers. Lee Adama is charged with solving the crime.
Roslin seeks to stamp out the black market by introducing new trade regulations.
A crazed Cylon Raider attacks the Colonial fleet in a series of hit-and-run attacks. Overworked Viper pilots must defend a mining operation from this Raider that they nickname "Scar."
A woman takes hostages on Cloud Nine and demands that Adama turn over Sharon in order to avenge her husband's death at the hands of the Cylons.
Apollo assists in the search for a missing Raptor team as the new commander of the Pegasus grows increasingly unstable.
After Boomer's consciousness is downloaded into a new body following her death, she struggles with her new life on Cylon-occupied Caprica. Number Six is asked to help Boomer adjust to her new role in Cylon society.
Chief Tyrol is plagued by terrifying dreams and seeks the aid of a priest. Kara leads a rescue mission to Caprica. Roslin and Baltar go head-to-head in a presidential debate that changes dramatically with the discovery of a habitable planet.
When Baltar wins the vote, Roslin considers stealing the election because she believes he is a Cylon collaborator.