Gaius Baltar (James Callis) believes the case against him is in tatters given the shattered credibility of key prosecution witnesses Colonel Tigh (Michael Hogan) and Laura Roslin (Mary McDonnell). The defense team of Romo Lampkin (Mark Sheppard) and Lee Adama (Jamie Bamber) is less confident after Gaeta (Alessandro Juliani) tells the court that he saw Baltar signing a death list on New Caprica. Lampkin’s surprise motion for a mistrial leads him to call Lee to the stand, in a move that could incriminate Admiral Adama (Edward James Olmos) himself. Meanwhile, eerie coincidences are being experienced aboard Galactica. The sound of a familiar but untraceable melody haunts several members of the fleet. President Roslin is also unnerved upon learning that her nocturnal dreams of the Kobol Opera House are shared by Sharon (Grace Park) and Caprica Six (Tricia Helfer). Whether a vision, dream or “projection,” Roslin suspects it’s the work of the mysterious Cylons known as the Final Five.

The trial of Gaius Baltar (James Callis) is underway. Unable to prove his role in the genocide of the Twelve Colonies, prosecutor Didi Cassidy (Chelah Horsdal) focuses on the charge of treasonous collaboration with the enemy on New Caprica that resulted in the loss of 2,600 human souls. With Lee Adama (Jamie Bamber) as his now-willing associate, Romo Lampkin (Mark Sheppard) opens the defense by arguing that the trial is motivated by mob bloodlust and Laura Roslin’s (Mary McDonnell) need for vengeance. But with a succession of powerful witnesses lined up to testify against Baltar – including President Roslin and Colonel Tigh (Michael Hogan) – the defining issue becomes how far will Lee go to question the word of the fleet’s leaders, while risking the increasing enmity of the chief judge: his own father, Admiral Adama (Edward James Olmos). And the Machiavellian Lampkin isn’t shy about exploiting Lee’s antagonistic relationship with the Admiral to gain an edge in the hostile courtroom. For his part, the Admiral must also deal with the possibility that the Cylons, conspicuous by their absence, have been secretly shadowing the fleet as it jumps from one sector of space to another, gradually closing in on the Ionian Nebula, the next stop on the route to Earth. Meanwhile, as each new jump brings the fleet closer to its destination, a series of strange hallucinations, visions and dreams begin bedeviling several members of the fleet, including President Roslin. By the time Roslin takes the witness stand, the stage is set for the trial against the “most hated man in the universe” to take a surprising twist.

With recent catastrophic events still fresh, the crew of Galactica is numb. Some are losing themselves in the bottle while others, specifically Lee, are unable to concentrate on effectively doing their jobs. Lee is pulled from CAG and assigned to protect Romo Lampkin (Mark Sheppard), an attorney called in to defend Gaius Baltar (James Callis) after his original lawyer is killed in what may have been an act of sabotage. Lampkin’s provocative tactics and the fact that he once worked for Lee’s grandfather – a storied defense attorney with a checkered past on Caprica – begin to revive the grounded pilot from his despair. When they narrowly avoid death in another bomb plot, Lee and Lampkin become closer. Caprica Six (Tricia Helfer), expected to testify against Baltar, has mixed feelings about her ex-lover, which Lampkin exploits masterfully. Meanwhile, the crew debates whether the bombings are the handiwork of a Cylon infiltrator, Baltar’s many foes or perhaps a radical inspired by his writings. When a third bomb goes off in Lampkin’s quarters, Lee discovers that the lawyer’s briefcase contains answers to more than one riddle.

As the fleet refuels near the stormy atmosphere of a planet, Kara (Katee Sackhoff) spots a Cylon heavy raider lurking in the dense clouds and chases after it. In a hair-raising dogfight, she feels her viper take multiple hits and the enemy ship escapes. But when Kara returns to Galactica, there’s no evidence of damage to her viper. Badly shaken and afraid she’s losing grip on reality, Kara cuts her next mission short by feigning a hydraulic failure. That’s reason enough for Lee (Jamie Bamber) to send her for a full medical and psych evaluation. It also has everyone wondering if Galactica’s top gun is cracking up. Kara is wondering the same thing. She’s haunted by nightmares about Leoben (Callum Keith Rennie), the Cylon who held her captive on New Caprica. The mandala she painted long ago keeps appearing in the planet’s atmosphere, drawing her toward its mystical vortex. And memories are flooding back about her abusive mother Socrata (Dorothy Lyman), an alcoholic ex-marine. Lee retains faith in his best pilot and keeps her on active duty. But the tightrope Kara walks between present and past, reality and illusion, threatens to snap.

When fuel contamination causes an accident that almost kills President Roslin (Mary McDonnell), an investigation reveals widespread discontent over working conditions on the tylium ship. Gaius Baltar (James Callis) is blamed for the political unrest when it is discovered that the tylium workers have been empowered by Baltar’s new book, a political manifesto that his lawyer has secretly been smuggling out of his cell. Concerned for the safety of the fleet, President Roslin and Admiral Adama (Edward James Olmos) order Chief Tyrol (Aaron Douglas) to crack down on the defiant tylium workers and get fuel production up and running as quickly as possible. But Tyrol, a former union labor leader, strongly identifies with the plight of the tylium workers, and is deeply troubled when he is forced to suppress the workers’ protests. Tyrol’s inner conflict builds until catastrophe strikes and Tyrol openly defies Adama’s orders and leads the workers in an all-out strike, which has more far-reaching consequences than Tyrol ever intended.

After 49 days without a Cylon sighting, there’s growing optimism that the enemy has lost the scent. Lee (Jamie Bamber) cracks down on any complacency by ordering his pilots back to hardcore training. With more downtime than usual on his hands, Adama (Edward James Olmos) is having vivid memories of his long-dead ex-wife Caroline (Lucinda Jenney) on the anniversary of their marriage. Meanwhile, gossip is spreading about the Admiral’s relationship with Laura Roslin (Mary McDonnell), as the two meet to discuss the trial of Gaius Baltar (James Callis). Elsewhere aboard Galactica, Tyrol (Aaron Douglas) and Cally (Nicki Clyne) are called in to repair a loading dock that had taken heavy fire during the escape from New Caprica. After inadvertently dislodging one of the patches, they find themselves trapped on the wrong side of an airlock as their remaining oxygen leaks away. Lee and Kara (Katee Sackhoff) attempt an unorthodox rescue before space can claim two more victims.

“Paranoid, pig-headed and argumentative.” That’s the Sagitarron race as described by Dualla (Kandyse McClure), a Sag herself. Showing clear signs of Mellorak Sickness, a group of Sag refugees stick to fundamentalist beliefs by shunning the booster shots that will prevent both their own deaths and a widespread epidemic. Inside “Dogsville,” the Galactica hanger deck that houses refugees, the toxic atmosphere turns even more hostile when Dr. Roberts (Bruce Davison) fails to save a series of patients who have unwillingly been given shots. Bucking against widespread hatred of the Sag minority, Helo (Tahmoh Penikett) discovers a long-standing pattern of suspicious Sag deaths. When Dualla catches the disease, her dramatically worsening condition confirms Helo’s worst fears and he must fight to get her into the care of Doc Cottle (Donnelly Rhodes). Meanwhile, Laura Roslin (Mary McDonnell) intends to charge Baltar (James Callis) with high crimes and treason. Zarek (Richard Hatch) warns her that the trial will trigger a “hurricane” of trouble throughout the fleet. While Baltar stews in his cell playing mind games with Number Six (Tricia Helfer), Caprica Six begins to experience similar psychic disturbances as a phantom Baltar whispers his own poisonous advice.

"Sleep deprived and on a hunger strike in his Galactica cell, Baltar (James Callis) tries hanging himself in the belief that he’s a Cylon and that resurrection will cleanse his soul. Gaeta (Alessandro Juliani) thwarts his suicide attempt, however, and Baltar lives to face an interrogation by Laura Roslin (Mary McDonnell) about his role in the original Cylon attack on the Colonies. His denials crumble when Caprica Six (Tricia Helfer) enters the interrogation room. She demands a public trial for her former lover, but Roslin and Adama (Edward James Olmos) opt to extract the information they’re looking for by injecting Baltar with potent hallucinogens. The extreme measures implemented on the former President reveal both his guilty conscience and his discoveries in the Temple of Five. Roslin and Adama task Gaeta with extracting more information from Baltar, hoping that the former presidential aide may still be trusted. However, they may have greatly underestimated the level of Gaeta’s resentment toward his former boss. Meanwhile, Kara (Katee Sackhoff) continues her pursuit of Lee (Jamie Bamber), promising she’ll leave Anders (Michael Trucco) if he splits with Dualla (Kandyse McClure). The pair seems destined to be together, but their respective spouses battle to keep the marriages intact. With Tyrol (Aaron Douglas) feuding with his own wife Cally (Nicki Clyne), matters of the heart are debated in the smoky confines of Joe’s Bar."

On the algae planet, Lee (Jamie Bamber) and Anders (Michael Trucco) prepare to fend off the Cylon assault on the Temple of Five – supposed site of the Eye of Jupiter, an artifact which the scriptures claim points the way to Earth. The task gets tougher still when Kara’s (Katee Sackhoff) raptor is hit by enemy fire and crashlands on the planet. With limited manpower and the Cylons in full force, Lee determines that they can’t afford to go after Starbuck. However, to stave off mutiny by Anders and his men, Lee must order his emotionally-conflicted wife Dualla (Kandyse McClure) to mount a rescue attempt. As the team of marines and civilians try to hold off the Cylon forces led by D’Anna (Lucy Lawless) and Baltar (James Callis), Tyrol (Aaron Douglas) rushes to make sense of the temple’s glyphs before the planet’s star explodes. Meanwhile, Sharon/Athena (Grace Park) infiltrates a Cylon baseship to rescue her hybrid baby, Hera.

While working on the algae planet, Tyrol (Aaron Douglas) discovers the Temple of Five, reputed to be the home of the Eye of Jupiter, which will guide the ones who discover it to Earth. His report is intercepted by the Cylons, who request a meeting with Adama (Edward James Olmos) and Laura (Mary McDonnell). Their proposal: let us have the Eye and we will let you leave unharmed. Adama’s counter-proposal: make any move to take the Eye and we’ll nuke the planet. The Cylons bring another piece of news: Sharon (Grace Park) and Tyrol’s (Tahmoh Penikett) baby is alive, but not well. Sharon is initially skeptical, but when Adama confirms that Laura hid the baby at her school, she and Tyrol being to make plans to rescue her. As the standoff continues, tensions rise in both camps. On the Cylon baseship, D’Anna’s (Lucy Lawless) sense that she and Baltar (James Callis) share a destiny that might not include the others sows dissension, while on the algae planet, efforts to protect the Eye are complicated by Lee’s simmering affair with Kara (Katee Sackhoff), especially since Lee (Jamie Bamber) is counting on Anders (Michael Trucco), Kara’s husband, to rally the civilians to the cause. Then the Cylons launch a flight of raiders, bound for the algae planet, forcing Adama to show he’s not bluffing.