A Cylon and his human prisoner enter into a bizarre domestic relationship as Col. Tigh's wife secures his release from a Cylon detention center and Admiral Adama prepares his diminished fleet for a dangerous rescue mission to New Caprica. The Cylons have now occupied New Caprica for four months, and the psychological toll their presence has taken on the human settlement is devastating. Meanwhile, Cylon Leoben is holding Kara Thrace prisoner in a fully furnished apartment. While Leoben believes he can win Kara's heart and mind, it's not going to be an easy process and he might have to die multiple times before doing so. Back in his barren cell, Col. Tigh has lost an eye after being tortured by the Cylons. When his wife Ellen secures his release by sleeping with Cylon leader Cavil, Col. Tigh swiftly returns to support the insurgency, where a disillusioned trainee named Duck has volunteered himself for a deadly suicide mission. Though somewhere deep in space Admiral Adama and his son Lee are at odds over the idea of a rescue mission to New Caprica, a startling revelation will bring them together and renew their determination to rescue the hopeless humans who have fallen under command of the Cylons.

The insurgency faces a grave threat as the Cylons crack down following Duck's explosive suicide mission and Admiral Adama prepares for a daring rescue mission. Convinced after Duck's attack that they will never be able to live peacefully with humans, the Cylon occupiers on New Caprica order the arrest of hundreds of suspected insurgents -- including Tyrol, Anders, and Tigh, who miss the round up while attempting to contact the Galactica from their clandestine headquarters. Later, after Tigh refuses Laura Roslin's request to cease the suicide bombings, another insurgent blows themselves up and President Baltar is forced to sign a death warrant for 200 suspected rebels. Back in the apartment where Kara Thrace is being held, Leoben introduces her to a little girl named Kacey whom he claims is the pair's biological child. Meanwhile, on the Galactica , Admiral Adama and Lee are at odds over Adama's decidion to select Cylon Sharon Agathon as the leader of the rescue mission. But as Ellen Tigh and Cavil meet for another tryst back on New Caprica, the manipulative Cylon leader draws out some key information about the insurgency by threatening to capture and torture her husband once again.

Part one of the two-part story arc "Exodus" gets underway as Sharon and her crew successfully deflect a surprise attack by the Cylons and Tyrol stages a daring mission to rescue a group of suspected insurgents from the Cylon firing squad. While these two events indeed provide the human population with a newfound sense of hope, uncertainty lingers over human and android alike as President Baltar hears his Cylon overlords pondering the prospect of simply nuking the colony and abandoning plans to live peacefully with humans. Meanwhile, as the insurgents learn of Ellen Tigh's complicity with the Cylons, Kara Thrace embraces her new role as a mother and Cylon D'Anna becomes convinced that her child is still alive. Back on the Galactica , everyone says their goodbyes as Admiral Adama prepares for his dangerous rescue mission to New Caprica. Should the insurgents on New Caprica prove successful in their plans to launch a massive attack in tandem with the rescue mission, perhaps the crews of the Galactica and the Pegasus will be able to meet up and celebrate their success as planned. But in order for the mission to truly succeed, Sharon must first mix among the Cylons in a daring bid to obtain the launch keys for the grounded Colonial ships that will carry the humans to safety.

The rescue mission to New Capricia gets off to an explosive start in the second chapter of the two-part "Exodus" saga. Though Lee is convinced that his father will perish in the mission, he is consoled by the sentiment that his father will live on as a great hero. Back on New Caprica, the insurgents wait for the uprising with baited breath as a heartbroken Col. Tigh poisons his wife Ellen. The first explosions lighting up the sky, the Cylons look out from Colonial One to see the city in flames. Outside, the humans are racing to their predetermined evacuation points as Anders, Tyrol, and Tigh launch an insurgent attack and Laura Roslin and others attempt to reclaim Colonial One. When the Galactica drops into low atmosphere to launch Vipers, the Cylons take the opportunity to surround it. Thankfully for Admiral Adama and company, Lee and the Pegasus crew arrive just in time to save them from certain doom - but at what cost? As Anders clears the detention center down on New Caprica, he comes across an unconscious Starbuck. Upon awakening from her slumber, Starbuck insists that she will not leave without Kacey. Realizing that they have lost control of the colony, the Cylons prepare to retreat, though they leave D'Anna behind to activate a nuclear bomb that will render the colony uninhabitable.

Three days have passed since the rescue mission to New Caprica, and the leaders of the insurgency are meeting in the bowels of the Battlestar to determine the fate of Jammer -- a human convicted of treason for his collaboration with the Cylon police force. With President Baltar absent, his vice president Tom Zarek assumes power and enters into negotiations with Roslin. But while Roslin and Zarek appear to have reached a common ground in regards to Zarek's role as president, Zarek has one order of business before relinquishing his throne. Somewhere on the Galactica , a secret tribunal is meeting to convict and execute those they deem to be the worst collaborators, but there's descent within the ranks; Anders and Starbuck are at odds over how to handle Gaeta, a development that could highlight irreconcilable differences between the couple. Could it be that Gaeta was actually a critical component of the rescue mission's success? Back on a Cylon baseship, Gaius Baltar awakens to discover that his fate is about to be determined by the Cylon leaders. When the jury becomes deadlocked, Baltar's fate rests in the decision made by Six.

As Baltar remains a prisoner of the Cylons -- who believe that the former president may be able to lead them to Earth -- the crew of the Galactica decipher Baltar's abandoned notes and set course for the same nebula that the former president is leading the Cylons to. But the battle for New Caprica has taken a heavy toll on the psyche of the survivors, and after Helo assists Sharon in picking her new callsign "Athena," Starbuck is grounded for taking some careless risks during training. Replaced as Admiral Adama's right-hand man by Helo, a disgruntled Col. Tigh struggles with how to get back into the admiral's good graces as Tigh and Starbuck bond over their mutual trauma. Meanwhile, Caprica Six educates Baltar about the Cylons' power of projection, an ability which allows them to see beauty wherever they wish. Gaius comprehends this concept far better than he would have ever expected to, leading him to agonize over the possibility that he may actually be a Cylon. Later, when a Cylon scout ship indicates that it has been infected with an incurable virus that kills all Cylon life, Gaius agrees to investigate in order to determine once and for all whether he is human or android.

Upon discovering a Cylon baseship adrift in the Lion's Head nebula, Apollo and Athena investigate and discover that a mysterious virus has decimated the Cylon crew. The few remaining Cylon survivors are rushed back to the Battlestar , where Doc Cottle develops a vaccine that can curb the effects of the virus with frequent injections. The prospect of being cured ultimately proves too much for sick Cylon Simon to deny, and in desperation he soon tells the Galactica crew everything he knows about Baltar's role in helping the Cylons find Earth. But back in the Cylon fleet, D'Anna and Caprica Six now believe that Baltar is leading the Cylons into the Nebula in hopes that they will become infected and die -- subsequently torturing him in hopes of eliciting a confession. Meanwhile, on the Battlestar , Lee Adama hatches an ingenious plan to decimate the Cylons by drifting into close range with a Cylon resurrection ship and killing the infected prisoners so that the disease will spread to the fleet when they download to new bodies. No doubt it's a brilliant plan, but is it a morally sound one?

Three Cylon raiders have jumped in the middle of the Galactica's fleet, forcing the crew to brace themselves for a fight. After Starbuck and Kat take out two of the raiders, however, Adama receives a desperate call for help from the third raider. Upon learning that Lt. Daniel "Bulldog" Novacek, who once served under Adama, is piloting the third raider, the admiral welcomes Novacek aboard. The Cylons had taken Novacek prisoner after a mission that he and Adama had taken part in failed. After escaping his captors, Novacek stole one of their raiders and shot off into space. Could it be that Adama and Novacek's mission was the very thing that provoked the Cylon's deadly attack on the Colonies? As Adama confesses an elaborate story to Lee, Col. Tigh reveals to Novacek that Adama was the one who ordered the missile strike that resulted in his being captured by the Cylons. Just as Starbuck begins to suspect that the Cylons actually wanted their prisoner to escape, Novacek attacks Adama in a violent bid for brutal revenge.

Bitterly estranged from her husband Sam Anders, Starbuck wanders below deck to observe a boxing match between Apollo and Helo. Helo emerges triumphant, and Starbuck challenges him to an inter-gender bout. Upon joining Adama ringside, closet boxing fan Laura Roslin learns that pugilism has been a longstanding tradition on the Battlestar for those seeking to settle lingering grudges. The latest matches have been largely over lingering issues concerning New Caprica. Meanwhile, relationships between those aboard the Battlestar get complicated after a groundbreaking ceremony held by President Baltar to celebrate the New Caprician colonization. After allowing some of his crew to leave and join the new colony, Adama challenges Tyrol to a few rounds in the boxing ring. Beaten badly, Adama seizes the opportunity to warn his crew that he will be decidedly more hard-hearted in the future. Later, Starbuck and Apollo step into the ring to duke it out in the evening's main event.

When the fleet's food supply becomes contaminated and Sharon discovers a planet rich in edible algae, Admiral Adama must make an important decision about how to navigate through the enormous star cluster that stands between the fleet and the valuable food source. Though the elaborate plan of shuttling groups through the cluster will indeed be difficult to execute, the desperate crew has little choice but to try. Meanwhile, Captain Louanne "Kat" Katraine attempts to hide her true identity when the past threatens to catch up with her, and Gaius Baltar attempts to construct a new identity while pondering the prospect that he is one of the five, human-form Cylons whose identity has never been revealed. As the attempt to reach the algae planet gets underway, the peril the fleet faces proves greater than anyone ever anticipated.