Starbuck's Viper is brought onto the deck in poor condition caused not by combat but by Prozna's repair job. Starbuck insists he get the repair job done, but learns he died in the fire with 84 others. As she leaves, Chief Tyrol informs her about Apollo's apparent death, and that Boomer is missing.
Boomer is piloting the Raptor in space, having successfully evacuated civilians. Firing out a communications drone, she hopes a Colonial warship will determine their location through the Cylon jamming. Elsewhere on board, Dr. Gaius Baltar is haunted once more by the Number Six, who quickly disappears once more.
On Galactica, the ship is prepared for an FTL jump. As procedure, the flight pods are retracted. Using an artificial wormhole, the ship instantly finds itself in orbit over Ragnar, close to the Anchorage.
Roslin's fleet has survived the nuclear explosion, though Roslin and the Colonial One crew were briefly knocked out. Running down to the cargo bay, they attend to Apollo, who explains he used Galactica's electric-pulse coils to trigger an early detonation of the missile, tricking the Cylons into thinking it exploded on contact.
Galactica moves into Ragnar's orbit, passing through the eye of a storm. Starbuck returns to her bunk, where she tearfully prays to the Lords of Kobol over a photograph of Apollo. Cpt. Kelly passes through the hanger deck, taking dog-tags from men and women under his command as more bodies are brought in. Galactica successfully docks with Ragnar Anchorage, and Tyrol leads Cally and other deckhands to recover the munitions, as Marines -still in fatigues- search the area. They are confronted by an armed man.
On Colonial One, Boomer's Raptor successfully docks and disembarks its passengers. Boomer warns Apollo that Cylons are somehow shutting down the systems of the more up-to-date vessels, having received on the wireless that obsolete craft have fared better. As Baltar leaves the Raptor, he is introduced to Roslin to serve as a scientific adviser, while Boomer is ordered to jump around the system and bring FTL-capable civilian ships to the fleet.
On Ragnar Anchorage, Tyrol tries to calm down the armed man, who is unaware of the war. The man demands to have access to a ship he can escape in, but gives up and is disarmed.
Baltar sits on the passenger deck, studying the recent changes to the CNP. He is visited again by the Six from before, but he insists she is merely a figment of his imagination, though she suggests there is a chip in his head. While she gives him some help, she also offers him her love and kisses him, before disappearing again.
On Ragnar Anchorage, Adama discusses matters with the man, who shows him around. He explains away his missing space-ship as being on the other side of the space station, and that he is an arms dealer who was stealing from the depot. As the two examine a crate of nuclear warheads, a bomb being transported by the crewmen detonates. The two survive, but are cut off by debris and must find their own way back to Galactica.
Roslin's fleet is complete, with Boomer bringing the last of the ships she can find. Roslin briefly visits the passenger liner, Botanical Cruiser, where she negotiates supply and power distribution with the captain. She talks with Cammy, a Caprican girl who is unaware of the attacks, before leaving for Colonial One. A Raider jumps nearby and then leaves, meaning the Cylons now know the location of the fleet. In an emergency meeting, Doral is opposed to abandoning the sublight ships, while the captain insists they transport as many people as possible to the FTL-capable ships. Time is limited, and Roslin concedes to Apollo's recommendation they simply abandon the sublight refugees and jump to Ragnar before they too can be destroyed. Along with Billy, Roslin reveals her cancer diagnosis, and feels sick with herself for only thinking about it and not the wider picture. Billy informs her Botanical Cruiser is a sublight ship, meaning Cammy will die. The FTL ships are quietly sent coordinates to Ragnar to avoid the sublight ships even trying, which would risk exposing them if boarded. The radio messages are filled with pleas for mercy, prayers, and calls to "rot in hell" for the betrayal. The Raiders jump in and fire enough nuclear missiles to destroy every ship within seconds.
On Ragnar Anchorage, Adama and the man continue moving through accessways. The man, already sweating earlier, is now suffering painful headaches and is too tired to walk straight. He comments on mankind's folly and that God created the Cylons to make up for the mistake, though Adama is not interested in such talk.
At CIC, Tigh is briefed by Gaeta they have another three hours before they can expect a full resupply. Dualla reports the arrival of the civilian fleet, which briefly sends Galactica to Action Stations until they are confirmed civilians. Roslin comes abroad Galactica to meet with Tigh, and tries to convince him the war is already over and Galactica's priority should be to protect the refugees. Tigh refuses the order, but concedes to two disaster pods being given to the civilians, and orders Apollo to the flight deck as their new CAG. Tyrol returns from the Anchorage with supplies and has a crewman report to Tigh on Adama's whereabouts. He sees Boomer pass the man and they embrace. Baltar and Billy make their way through the ship looking for CIC and run into Dualla, who kisses Billy and gives him the tour as before. Apollo reaches the hanger to meet Starbuck, who is having to fix her Viper by herself. He heads off to the Squadron ready room, and takes up Starbuck's request he inform Adama he is indeed alive.
On Anchorage, Adama and the man continue down a flight of stairs. The man reveals he has no allergies, and Adama understands the truth. He is some kind of humanoid-model Cylon and Ragnar's radiation is causing problems for his body. He thinks Adama already knew about the radiation and has led the Colonial Fleet into Ragnar for protection. Finally, he reveals he is capable of uploading his consciousness upon death to a server and resurrect into a new body. Adama believes him, but doubts he personally can do so, suspecting the radiation is preventing it, leaving him to die a slow death. The man attacks Adama, and they fight over hot pipes. Though the man has superior strength, Adama is able to best him and beat him to death.
In CIC, Baltar explains to Gaeta that the Cylons used CNP to infect the Colonial Fleet ships with a computer virus. Gaeta adds that as Galactica has not got CNP up and running due to the lack of networking, but the installation tool is around. The Six appears over him and mocks him for his hubris and narcissism, and he struggles to hold a conversation with both her and Gaeta at once. As Gaeta goes back to work, Six shows Baltar around CIC and steers him towards a Cylon device planted on the DRADIS console. He concludes there must therefore be another Cylon agent on the ship.
Baltar begins walking around CIC to get a closer look at the device, but cannot reveal what it is without having to explain how he knows about it. Doral interrupts Baltar as Six teases him, and convinces him someone must be implicated as a Cylon agent to get the device revealed. He considers Doral, how he is not a member of the crew but has had unrestricted access to CIC for weeks, meaning he very well could be the agent. Nearby, Adama is being looked over by a medic as two Marines bring in the man's body. Tigh is informed about the existence of Humanoid Cylons, and reveals to him about Apollo's survival. Adama finds his son waiting for him in his office.
Baltar meets with Tigh and Adama on the autopsy results for the man on Anchorage. The results confirm him to be synthetic in origin, meaning there could be many more Cylons in the fleet that resemble humans. Baltar feigns ignorance and offers his services to the military in finding more Cylons. He is ordered to absolute secrecy to prevent Galactica and the fleet falling to paranoia.
In the hanger, Starbuck is ready to launch on a reconnaissance mission. She reveals to Apollo his brother Zac failed his Basic Flight course and she passed him due to their relationship.
Kelly and two Marines arrest Doral as he walks around Galactica. Baltar explains to Tigh he performed discrete tests on everyone in CIC and identified Doral as synthetic. This gives him the opportunity to casually bring up the device on the DRADIS console, which Doral denies knowledge of. Tigh leaves the room to observe the device's removal. Gaeta apologises for not informing him of the device, which he noticed a week earlier but presumed to be part of the museum. The device is taken over to Baltar for study, and Tigh orders a search of the ship for any other mystery equipment that "just appeared".
Starbuck flies out of Ragnar's atmosphere through holes in the storm, soon falling out of radio contact. In orbit, she confirms there to be Basestars lying in wait.
Adama meets with Roslin as she discusses resupplies with Billy. Their new item of discussion is what to do with the convicts on Astral Queen, and Roslin refuses its captain's suggestions of summary execution. When he leaves, Roslin demands to know if Adama will stage a coup; when he denies this, she takes it as confirmation that she is the recognised President. Adama still, however, refuses to commit Galactica to protecting the fleet, and suggests they stay in the atmosphere while Galactica fights the Cylons. Roslin rejects his idea, and insists they must instead abandon the star system behind and take the 50,000 survivors to another planet to settle on.
Starbuck flies into the storm to warn CIC of two Basestars and heads back. Adama and Tigh discuss the new developments, theorising the Cylons did not feel they needed the whole fleet and can starve them out with only two. Due to the radiation interfering with the fleet, Galactica also must leave the storm and approach the Basestars before it can jump. Apollo, Tigh and Adama change to talking about the civilian fleet. Leaving them in Ragnar is no longer viable, and they cannot accommodate 50,000 on the ship. They have no choice now but to fight the Cylons in orbit and escort the civilian ships out to the distant Promar Sector. Galactica prepares to leave Ragnar Anchorage, and leaves Doral behind.
Galactica leads the fleet out of the storm, and readies its weapons. Its point defence turrets begin firing, creating an anti-air wall to keep the Raiders and missiles away, while railguns fire explosive shells at specific targets. The Vipers are launched and engage Raiders on the other side of the firewall. Two are destroyed and Apollo's is damaged but operable. The Cylons are distracted in their fight, which allows the refugee fleet to exit the atmosphere and jump away. Galactica is hit multiple times by missiles striking the flight pods, and it becomes clear that if they stay any longer it will be unable to function as a battlestar. The Vipers are ordered to land, with Starbuck pinning her Viper with Apollo's to push it into the flight deck.
In the aftermath of the battle, Adama attempts to lift the morale of the surviving humans by announcing plans to reach a legendary thirteenth colony, "Earth", whose existence and location have been closely guarded military secrets. Roslin later convinces Adama to privately admit that his announcement was simply a ploy as she believes Earth to be a myth.
Adama finds a slip of paper in his quarters with the typed statement, "There are only 12 Cylon models.". On Ragnar, Doral clearly appears to be suffering from radiation poisoning that has been shown to affect only Cylons. His identity as a Cylon is confirmed when a group of Cylons, including the metallic Cylon Centurions and several humanoid Cylons consisting of multiple copies of the Number Six, Doral, and Ragnar arms-dealer models, come to retrieve Doral. In a twist ending, one of the group appears to be Boomer, indicating that her counterpart on the Galactica is a Cylon as well.
- Story By:
- Teleplay By:
- Directed by: Michael Rymer