Season 2, Episode 01:
Galactica's CIC is in chaos, as everyone struggles to understand what just happened. As Bill lies bleeding out on the table, Lee yells out for someone to get Doctor Cottle. Suddenly, the crew is surprised when a Cylon Basestar jumps into the area and deploys fighters. Tigh orders an emergency jump, only for Galactica to jump somewhere else, on its own and without any of the other fleet ships.
Boomer tries to comprehend what she just did, while Tigh orders both her and Lee to be taken to the brig. He discovers that Cottle was on another ship when they jumped, and won't be able to come over until they reunite with the fleet. Medics arrive and take Bill to Galactica's infirmary.
On Kobol, Baltar looks on at the "shape of things to come", and is very confused. He asks HeadSix if the child is real, and she states that they are its parents and that the child will be born soon. He soon awakens in the midst of the ruins, and makes his way back to the crew of the crashed Raptor.
When he arrives, Baltar discovers that Socinus was seriously injured in the crash, and that Cylons may be in the area. Although Tyrol asks to collect more supplies, Crashdown overrules him and tells everyone that they have to hide in the forest.
Lee is put into a cell and tells Roslin about what happened to his father. Meanwhile, Tigh changes his blood-stained shirt as Ellen asks him what's going on. He tells her about the situation, and she hastily blames Gaeta for not transmitting Galactica's coordinates to the rest of the fleet. He tells her not to be hasty, but she counters that he is now in charge of the fleet, despite the fact that he doesn't want the command.
As Tigh walks to the CIC, he has brief flashbacks of his first meeting with Bill many years earlier, just after the first Cylon War. As he arrives in CIC, he tells the crew that Bill is still their commander, and that he will not let him die. Gaeta draws up a plan link the ship's navigational computers to find their fleet's current location, although doing so will risk the ship being compromised by the Cylons.
On Caprica, Kara is coming to terms with seeing another copy of Sharon, and threatens to shoot her again until Helo pushes her arm out of the way. Kara tells him that Sharon can't be trusted, but their conversation is halted when Sharon leaves the museum and flies off with the captured Raider.
On Kobol, the team is heading through the forst when Tyrol and Specialist Seelix realize that they left vital medical supplies for Socinus back at the crash site. Crashdown orders another specialist, Tarn, to go back and retrieve it alone, but Tyrol and Cally convince him to let them go as well. They head back to the site and retrieve the supplies, but not before a Cylon landing party discovers them. Tyrol and Cally manage to make it to the treeline, while Tarn is killed during the escape.
Tigh visits Galactica's sickbay and meets with the onboard medic, who tells him that Bill lost a lot of blood. She asks for Cottle's help, but Tigh tells her to make do with what she can. He then heads to the brig and interrogates Boomer, who claims that she still doesn't know what's happening. Tigh beats her, grabs a sidearm from a nearby Marine and threatens to shoot her, but is stopped when he has a flashback that causes him to lose his focus.
Heading back to the CIC, Gaeta gives Tigh their plan: Galactica will jump in and have the CAG hold off the Cylons for 10 minutes while the navigational computers calculate the fleet's location. Afterwards, Tigh conditionally releases Lee so he can continue his job as the CAG.
Galactica jumps back to their previous location, and is attacked by the Cylon Basestar. As Lee, Kat, Hot Dog and others fight in their Vipers, the medics in the infirmary work to save Bill's life by doing an impromptu heart massage while repairing the damage. During the battle, Lee destroys a Cylon Heavy Raider, which crashes into the ship's starboard flight pod. The calculations are completed just as the Cylons breach the network, and the ship jumps to the new location, where they are relieved to discover the other fleet ships.
Tigh orders Cottle to be brought over to Galactica, while telling the stabilized and unconscious Bill that he can't die, and that he needs his help more than ever.
Meanwhile, in the damaged flight pod, several Cylon Centurions make their way out of the crashed Heavy Raider and walk into the ship
- Almost Lethal Weapons: Whereas the same pistol has killed several Centurions and humans in a single shot before, the bullets Boomer fires into Bill's chest only damage his spleen.
- The Bus Came Back: Captain Kelly, who wasn't seen since the miniseries, steps up to take charge when Lee is put in the brig.
- Cliffhanger: The Cylons walking out of the Heavy Raider onboard Galactica.
- Dreaming of Things to Come: Baltar in the Opera House.
- Freeze-Frame Bonus: As Gaeta pulls out the networked wiring under his console, his display shows for a split-second that the Cylons broke through all of the established firewalls.
- Hollywood Hacking: Apparently, just the act of linking the Galactica's computers together makes them vulnerable to the Cylon virus.
- Interrupted Suicide: Tigh planning to set his medals on fire in the flashback was, according to Ron Moore, supposed to be a suicide attempt that's interrupted by Bill's arrival.
- Lady Macbeth: Ellen tells her husband that he will have to lead the fleet, in spite of the fact that he doesn't want to.
- My Gods What Have I Done: Tragically, Boomer reverts back to her human personality right after shooting the Old Man.
- Point Defenseless: Galactica deploys an improvised barrier of flak suppression defenses while holding off the Basestar. While it doesn't damage Lee's Viper, it fails to stop the Heavy Raider from crashing into Galactica's flight pod.
- Screw the Rules, I Have Connections!: In a flashback, Bill tells Tigh that he was able to transfer off the freighter he was stationed on because his wife had connections at the Defense Committee.
- Shout-Out: Tigh's flashback where he has a breakdown is intended to be a nod to Apocalypse Now.
- Survivor Guilt: Tigh expresses this in his monologue to the unconscious Bill at the end of the episode, and states that he should have died during the attacks.