Four months into the Cylons' occupation of New Caprica and the refugees of the apocalypse now live in constant fear. Col. Tigh leads a resistance movement on the planet while awaiting the return of Galactica, but Admiral Adama has problems of his own with a skeleton fleet, ill-prepared fighter pilots, and a pervasive softness that affects his own son.
A rash of suicide bombings sparks the Cylon occupiers to begin rounding up civilians in an effort to flush out the insurgents. Meanwhile, Starbuck discovers that she's being held hostage because the Cylons harvested one of her eggs to create a child, with her captor Leoben as the father; Adama plans an operation to liberate the New Capricans, but orders Lee and the Pegasus to continue the search
The insurgents rescue Roslin, Zarek, Cally and others from the Cylon firing line just as Boomer makes contact from Galactica; Three experiences a prophetic dream that reveals the Cylon-Human hybrid is still alive; The crews of the Galactica and Pegasus say their farewells on the eve of the attack; The Cylons reveal to Baltar that if they can't stop the insurgents, they will simply nuke the entire
The evacuation plan goes into effect, but not everyone is going to make it off New Caprica. Tigh has to do the unthinkable; Kara gets caught up with Kacey; the Cylons plan to nuke the planet and everyone on it; Galactica finds itself overmatched; Lee makes a tremendous sacrifice; and, Three finds baby Hera.
A shadowy group begins eliminating refugees of New Caprica who served with the Cylon during the occupation, and soon set their sights on Gaeta. Meanwhile, Starbuck's trauma causes her to lash out at Anders, forever changing their relationship; Baltar awakens aboard a Cylon base ship and is helpless to change his situation or save his relationship with Six.
Tigh and Kara begin to divide the crew between those who were on New Caprica and those who remained on Galactica, with troublesome results; Baltar convinces his Cylon captors to keep him alive by helping them locate Earth. When a Cylon ship finds an astronomical marker that will put the Cylons on the path to Earth, it becomes infected with a deadly virus, one that Baltar learns is ancient and might have been left behind by people from Earth.
Galactica investigates a drifting Cylon base ship filled with dead or dying Cylons. Aboard ship, Doc Cottle determines they contracted encephalitis from an adrift beacon, presumably left behind by the thirteenth colony -- Earth.
The Galactica picks up a fleeing Cylon raider that happens to be piloted by a Colonial officer thought to be dead. His return stirs up some ugly memories for Adama and Tigh, which the latter uses to rile up the injured officer in the hope that Adama might lose control of the situation. Meanwhile, Three believes she's made a remarkable discovery about life and death: she may have found Heaven.
The crew partakes in a boxing tournament where rank doesn't matter. In the ring, tensions between shipmates get to be resolved, sometimes with troublesome consequences: Adama hasn't forgiven Tyrol for leaving to settle on New Caprica, while Tyrol resents Adama for wanting him to remain aboard Galactica; Apollo and Starbuck resolve their true feelings for one another as they beat each other sensel
With the fleet's food reserves contaminated, Adama decides that they should journey through a radiant star cluster with fatal levels of radiation in order to get to an algea-rich planet.
On the algae planet, Tyrol finds a temple that might hold the Eye of Jupiter, the clue that will point its possessor in the direction of Earth. Since the planet is believed to be the last settlement of the thirteenth colony, D'Anna hopes she can see the face of God by entering the temple, while shifty Baltar wants to learn if he is one of the final five Cylon models.
Lee and Sam try to keep the Cylons from reaching the temple in order to give Tyrol enough time to decipher the glyphs and locate the Eye of Jupiter. Meanwhile, Athena uses the power of Resurrection to get aboard the Cylon baseship that has her baby and, along with Six, they escape from the ship and return to Galactica; Lee orders Dualla to locate Starbuck's crashed Viper; Three damages her relati
President Roslin and Admiral Adama try different strategies in order to get captured Cylon collaborator Baltar to reveal what he knows about the Cylon's intelligence regarding Earth.
Helo's stuck in the hangar bay with sick refugees whose sudden deaths prompt him to investigate the civilian doctor treating them. But he gets no help from the Galactica officers, who feel Helo has sided against them one too many times.
Adama has trouble letting go of his estranged ex-wife on their anniversary, but his troubles don't match the currently married Chief Tyrol and Cally, who have both been trapped in an airlock that is quickly venting into space.
Chief Tyrol is reassigned to oversee the refinery ship that supplies the fleet with fuel. But upon his arrival, he witnesses first hand the terrible working conditions these workers must endure.
Starbuck's dreams about the Cylon Leoben and the mysterious symbol found in the temple on the algae planet lead her to explore the nature of her life and recall her painful past with her abusive mother.
A bomb goes off, killing Baltar's defense attorney. Adama assigns Lee to provide security for his replacement, a man named Romo Lampkin, who once worked for Lee's grandfather.
The trial of Gaius Baltar reveals to the fleet that Col. Tigh killed his wife for collaborating with the Cylons and that President Roslin's cancer has returned.
The trial of Gaius Baltar comes to an end, with the tribunal reaching a verdict of not guilty. Meanwhile, Laura's dreams involving Hera, Six and Sharon at an opera house become more intense, so much so that the others in the dream also experience it; Baltar gets whisked away into safety by a group of people within the fleet who believe he is a savior with healing powers; Tigh, Tyrol, Tory and And