Following the destruction of the Colonies, the refugee fleet led by Galactica has been relentlessly chased by the Cylons who pop up every 33 minutes to attack again, and have been doing so for five days straight. 33 minutes gives them barely long enough to calculate a jump and distribute the coordinates to each ship. The perpetual attacks and jumps to escape prevent anyone from sleeping for very long, even if they aren't involved in keeping the fleet moving. The equipment is also stressed to the point that, finally, a passenger ship called the 'Olympic Carrier' is left behind, rebooting their jump computer when the jump is executed. When the Olympic Carrier suddenly jumps in to rejoin the fleet some time later, it seems certain that the ship must have been infiltrated.

Boomer awakes in Galactica completely wet and when she seeks a towel in her bag, she finds a bomb. She disarms the detonator and when she brings them back to the arsenal, she finds that six other detonators are missing. While the trembling Boomer is telling Chief Galen Tyrol about her findings, the portside tanks of Galactica explode. With the loss of 60% of the water provision, Commander Adama rations the supply and sends the Raptors to search water in the nearby planets. Meanwhile in the destroyed Caprica, Lieutenant Helo is rescued by another version of Boomer.

A prisoner questions the government and leads an uprising with the other prisoners with an attack on the way that the government is run.

A freak accident on the Galactica Flight Deck leads to the death of 13 pilots. 'Starbuck' is charged with training new pilots, but must first put to bed the guilt she still holds over the death of her fiancée, Zak Adama. Meanwhile, back on Caprica, 'Helo' and 'Boomer' find the source of the military signal.

Starbuck is hit by a Cylon raider and falls in an inhospitable moon with about 46 hours of oxygen supply. Meanwhile, Commander William Adama and Captain Lee 'Apollo' Adama lead a rescue mission, using all the possible resources under the protest of President Laura Roslin that orders to call off the mission. Meanwhile in Caprica, Helo is attacked in the shelter while preparing the breakfast for Boomer and him.

Chief Tyrol and Boomer have an love encounter covered by Tyrol's team and Sharon leaves one hatch open, giving access to the Galactica's arsenal. A copy of the Cylon Doral finds a breach in the security system of Galactica and blows up the bombs tied to his body, killing three humans and leaving thirteen wounded persons. Commander Adama decides to make public the information that Cylons now resemble humans with the support of President Roslin, bringing mistrust, paranoid and panic to the survivors. Sergeant Hadrian is assigned to investigate the case and bring the suspects to an independent court. She finds inconsistencies in the testimony of Chief Tyrol and his crew about where he was during the bombing. Meanwhile on Caprica, Helo seeks out the other version of Boomer, playing like a puppet to the Cylons.

When Dr. Gaius Baltar is called to the bridge of Galactica, he discovers that Cylon Number Six is visible for Commander Adama and the crew. Further, she claims to be Shelley Godfrey, who worked in Caprica security system, and that has evidences that Dr. Baltas is a traitor that allowed the Cylons to invade the human's defense mainframe and planted a bomb to destroy the system. Dr. Baltar temporarily loses his privileges and Lieutenant Gaeta is assigned to authenticate the proofs. Chief Tyrol asks Starbuck to help him to activate the Cylon raider. Meanwhile, in the Cylon-occupied Caprica, Helo and Boomer are in love with each other.

The Gemenon Traveler informs Galactica that a copy of Leoben Conoy has been captured. Commander Adama assigns Starbuck to interrogate the prisoner and advises her that this model cannot be trusted. Leoben claims that has planted a nuclear warhead in one spacecraft and Starbuck tortures him trying to discover where the bomb is planted. Meanwhile Boomer asks Dr. Baltar to be tested in his Cylon detector.

When Dr. Baltar finishes his Cylon detector, President Roslin that suspects that Commander Adama may be a Cylon suggests the commander to be the first to be tested. Further, she asks Billy to get information about behavior dating Dualla. She finds that Adama has sent classified messages and has flown in a Raptor in secret missions. When a Cylon raider suddenly approaches Galactica with erratic flight and Adama vanishes, President Roslin increases her suspicion. However, Adama return with Colonel Tigh's missing unfaithful wife Ellen Tigh, who was unconscious on board of the Rising Star, raising the suspicion that she could be a Cylon. Meanwhile in occupied Caprica, Boomer is in love with Helo and escaping to save his life.

When the Tylium reserve of the fleet is running out and enough for two more jumps only, Boomer and Crashdown find a deposit enough for a couple of years in an asteroid. However, the Cylons are exploring and processing the fuel in a well protected refinery with a base with many raiders. Commander Adama decides to attack the base and asks the unconventional Starbuck to analyze their strategy with eyes wide open and based on Dr. Baltar's guess. President Roslin, who is delusional and suffering hallucinations with the treatment with chamalla, agrees with the plan. Meanwhile in Caprica, when Helo sees Number Six alive after dying on his hands, he questions Boomer what might have happened.

The twelve representatives of the survivors of their colonies gather in the luxury liner Cloud 9 for a meeting to discuss political issues. Sagittarion selects Tom Zerek to represent their interests and the former terrorist raises the need of a Vice-President in case Roslin has any problem. His proposal is accepted and he becomes the only candidate. President Roslin gives her best effort trying to find an opponent and promising that Tom Zarek would never be her Vice-President. Meanwhile the abusive Captain Apollo, who is in charge of security with Starbuck, turns off the speech of Zarek, creating confusion with his followers, and accidentally they find a man with a weapon. In occupied Caprica, Helo discovers the truth about the evolution of the Cylons to the human form.

Starbuck has one night stand with Dr. Baltar, creating tension with Apollo. Meanwhile, Boomer and Crashdown find a habitable planet with ancient ruins and people conclude it is Kobol. President Roslin has visions with the pictures of the surface of Kobol and Elosha gives a religious interpretation to her visions based on the scriptures. Commander Adama sends three raptors to research the planet, but they are surprised by a Cylon starbase and the raiders destroy raptor number three, the number one crashes on Kobol and the number two jumps back to Galactica. Adama plots a scheme with Starbuck to lure the Cylons using the raider they have but President Roslin convinces her to jump back to Caprica to retrieve the mystic Apollo's Arrow to help her to lead the survivors to Earth. Meanwhile Boomer tries to commit suicide in Galactica while her copy is shot by Helo in Caprica.

When Commander Adama finds out that Starbuck was convinced by President Roslin to jump back to Caprica to retrieve Apollo's Arrow, he orders his men to arrest Roslin. They invade Colonial One and Captain Apollo does not obey the order and is also arrested for mutiny. Commander Adama also sends Boomer and Racetrack in a raptor with a Cylon transponder to drop a nuke on the Cylon starbase. However the bomb does not disengage, forcing Boomer to land in the starbase to release it manually. While on the deck, she discovers a secret about her origin. In Caprica, Boomer tells Helo that she is pregnant while in Kobol, Number Six exposes to Dr. Baltar the plans of God.

Adama is dying after Boomer's attack, but Dr. Cottle is on another ship, the Rising Star. The arrival of a Cylon Basestar however forces the fleet to make an emergency jump. Suddenly Galactica is alone. The fleet had old coordinates and jumped elsewhere. The only way to find out where they went is to jump back to the Basestar. Gaeta thinks of a dangerous plan. Back on Caprica Starbuck doesn't seem to like Boomer. Helo has a lot of trouble preventing her from killing the bearer of his child. Boomer is forced to flee. On Kobol things are getting precarious. The Cylons are getting close and the away team has to run, forgetting a medical kit with serisone the seriously injured Socinus needs.

The fleet has been reunited with the Galactica. However, in the process of finding the fleet, a cylon virus has penetrated the computers onboard the Galactica and it has also been boarded by centurions. Lee is let out of the brig and takes a team to stop the centurions. On Kobol, Chief returns from a mission with medical supplies for a dying Socinus, but will he make it?

Doc. Cottle is trying to save Adamas life whilst Tigh has some problems being in command of the fleet. On Kobol, a mission is being prepared to destroy a Cylon battery and escape the centurions. Things go wrong when non-combat personnel decide to sit out. Lee leads the rescue mission to Kobol but will it be too late for the Chief?

Martial Law is slowly dividing the fleet. A mission leads to disaster when civilians accidently get killed. Helo and Starbuck meet the resistance on Caprica lead by Samuel T. Anders. Lee schemes to free President Roslin. Tigh does not shoot down Lee because it is his friends only Son. Baltar uses Sharon's love for Tyrol to interrogate her.

Starbuck is wounded while on occupied Caprica, and she wakes up to find herself in the care of a doctor. Her suspicions are aroused when she never sees anyone else and when the doctor encourages her to have a baby.

Lee and Kara are reunited but trouble stirs when another copy of Sharon crosses Lee's path, will Helo shoot Lee to protect Sharon? They land on Kobol and start their long trek to find the Tomb of Athena. Adama replaces his CAG with Lt. "Catman" Birch whose first job messes up.

Commander Adama, Billy and the Chief join Laura Roslin, Apollo, Starbuck, Helo, the copy of Sharon and Tom Zarek in Kobol where they're looking for the Tomb of Athena. While Zarek and his buddies try to persuade Sharon to kill the Adamas, Gaius Baltar in Galactica tries to discover if his visions of Number Six mean he's really mad.

After releasing a video which shows the Gideon massacre, a journalist from the fleet called D'anna Biers is given full access to Battlestar Galactica by Commander Adama and President Laura Roslin, in order to show the human, true face of the Galactica crew. But are these D'anna's real intentions?

The Galactica crew decide to construct a whole new type of spaceship as a way to fight boredom demoralization. Meanwhile, they discover the Cylon virus that had attacked the Galactica intra net has learned about the battlestar and is able to kill them by taking control of it.

Galactica meets Pegasus, and Adama's command is threatened when the captain of Pegasus outranks him. A joyous celebration turns sour at some of the secrets emerging out of the differences of the two crews, and Baltar meets a familiar Cylon prisoner aboard Pegasus.

The Vipers from Galactica and Pegasus are about to start a battle, but they stop when Starbuck appears in the Black Bird carrying pictures of the mysterious Cylon ship. In Pegasus, the Number 6 prisoner tells Gaius Baltar about it.

Galactica and Pegasus prepare the attack against the Resurrection Ship, led by Starbuck, now a Captain. But Starbuck has their own trouble: she might be forced to kill Admiral Cain, while Cain is also planning to murder Commander Adama. Meanwhile, Gaius Baltar starts getting obsessed with the Number Six replica that is kept in Pegasus.

President Roslin is in the final stage of her cancer and about to die. On her death bed she has memories of Caprica. Just before the Cylon attack she opposed president Adar on striking down a violent protest of teachers. As one of her last decisions she orders the death of Boomer's baby. She sees it as a danger to the fleet. Dr. Baltar tries to think of a way to prevent the abortion. Number Six reminds him he will be president soon. Meanwhile a firing test with vipers goes awry. Cally finds out the rounds of ammunition were tampered with. Apollo and Starbuck arrest Asha Janik. She tells she is part of a group that wants to negotiate with the Cylons about peace. Apollo finds out an attack is planned on a tylium refinery vessel.

Apollo and many of the other members of the crew are using the Black Market to obtain goods and services. Apollo falls for a young prostitute and vows to save her and her child while investigating the murder of one of the crew. This leads him to a rogue ship where he has to confront the bad guy as well as confronting his own desires and past mistakes.

The fleet has discovered an asteroid field with a large ore deposit, enough to construct at least two new squadrons of vipers. But the Cylons know about it and behind every rock there could be a raider. Since the destruction of the Resurrection ship they changed their tactics from mass to sneak attacks. Several pilots are already dead and especially raider Scar is feared. Meanwhile Starbuck hasn't been herself lately. She drinks a lot, thinks much about Anders and is getting irritated by Kat. She continually challenges her, beats her record in training and calls her the next Tigh. Both claim they will hunt down Scar. 200 cubits and the precious Top Gun trophy, currently in Starbuck's possession, are at stake.

The relationship between Apollo and Dee becomes known to Billy when he catches them together on a date in a bar. While here, a terrorist attacks and holds the people hostage and threatens to murder them unless Adama hands over the Cylon prisoner.

Starbuck and Apollo come into conflict with one another about their differences of opinion and work ethic. Starbuck takes a lecturing from the commander of Pegasus about fighter pilots disappearing on a mission.

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. Some soul-searching is done by Number 6, the Sharon clone, and Lucy Lawless' character in the way that humans are treated and the definition of love. This story explores the Cylon world.

The presidential elections are coming and it's looking good for president Roslin. Dr. Baltar is way behind in the polls and he and his campaign leader Tom Zarek try to think of a way to turn things around. Meanwhile Starbuck is finally able to plan a rescue mission for Anders and his people on Caprica. With the help of Cylon technology and Boomer, Caprica can be reached by raptors in only ten jumps. On the first jump something goes immediately wrong. Racetrack's raptor jumps to the wrong coordinates. She discovers a habitable planet, hidden in a nebula. Chief Tyrol seems to be in a lot of psychological distress. He beats up Cally and has every night the same scary dream. He asks advise from a rather unconventional religious counselor.

The group on Caprica is under heavy fire by the Cylons, but suddenly they stop. A while later the attackers seem to have completely disappeared. Starbuck and the others set off for the Galactica, but unknowingly bring a Cylon on board. It's a copy of Cavil, the religious counselor of Tyrol. He has a message and tells the Cylons now think the attack on the colonies was wrong and they will leave mankind alone. Meanwhile the presidential election has completely shifted in favor of Dr. Baltar. Only one ship's votes are left to be counted and president Roslin is way behind. Then a miracle happens.

Tigh, Tyrol and Anders lead the Resistance on New Caprica to increasingly deadly attacks against the Cylons. Kara finds herself trapped in a new life with Leoben Conoy, and Duck makes a fateful decision. Meanwhile on Galactica, Adama struggles with the question of whether to return to New Caprica to mount a rescue attempt.

Adama plans to return to New Caprica and drop off a surprising person to act as a liaison between Galactica and the Resistance. Tigh's insistence on the use of suicide bombers and ever escalating violence stuns even the fellow leaders of the Resistance. Eventually, the suicide bombings cause the Cylon occupiers to crackdown on their human subjects.

Sharon helps to organize the Resistance as Adama heads to New Caprica aboard Galactica for a daring rescue operation. Lee disagrees with Adama's plan to return to New Caprica, arguing that they need to focus on the survival of humanity. He sees the rescue mission as a one-way trip.

Tigh must decide the fate of his wife Ellen after the assistance she rendered to the Cylons. Lee struggles with his assignment to protect the civilian fleet on its journey toward Earth while Adama returns to New Caprica with just the Galactica. The Resistance coordinates an attack on the Cylons just as Galactica arrives. As the Cylons begin to lose control, Number Three (D'Anna Biers) vows to put a final end to the New Caprican experiment.

Tyrol participates in the Circle, a secret tribunal on Galactica that tries and convicts in absentia those accused of collaborating with the Cylons during the Occupation. The death sentences--administered without the knowledge of Roslin or Adama--begin to weigh on Tyrol's conscience. Baltar faces a similar jury among the Cylons, who must decide whether he is allowed to stay with them.

The Galactica encounters a Cylon Basestar devastated by a deadly virus. Lingering feelings of rage lead Saul Tigh and Kara Thrace to cause problems aboard Galactica between the survivors from New Caprica and those who stayed with the fleet during the Occupation. Baltar tries to convince the Cylons of his value to them in an attempt to stay alive.

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.

To help the crew of BSG let off a little steam, boxing matches are arranged. Helo and Apollo square off, seemingly venting their frustrations over a difference on opinion on wiping out the Cylon race by perpetuating a virus that only the Cylons are susceptible to. Starback (Kara Thrace) and her husband, Samuel Anders, are experiencing problems of their own since Starbuck was held captive on New Caprica with a Cylon captor. Anders expresses his desire to have Kara back. Starback and Apollo decide to go into the ring to slug it out - but is it resentment, or pent up feelings for each other that they yearn to let out?

Now onboard Galactica, Baltar faces charges of treason. He contemplates suicide with the help of Number Six. Questions remain about his true identity. Is he a Cylon or isn't he? Apollo shows off the new drinking establishment on Galactica, Joe's Bar, to Tyrol. Apollo thinks about Kara and wonders whether his marriage to Dee is worth saving.

The Colonial fleet and the Cylons engage in a costly battle within the Ionian Nebula, Gaius becomes the figurehead of a religious sect hiding on Galactica, and Starbuck's resurrection shocks and terrifies the fleet. Meanwhile, Colonel Tigh, Galen Tyrol, Sam Anders, and Tory Foster struggle with the revelation that the are Cylons.

The Cylons are bitterly divided over how to deal with the Cylon Raiders, who refuse to attack the Colonial Fleet because of the recent detection of the Final Five within said Fleet. Meanwhile, Admiral Adama and crew send Lee Adama off into his new life as a member of the Quorum of Twelve, and Adama has to deal with the possibility that Kara Thrace may very well be right about her knowing how to get to Earth.

The aftermath of a coup among the Cylons leads to further conflicts, Lee finds himself facing off against Roslin at his first meeting with the Quorum of Twelve as the 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.