Talented but cocky pilot William Adama graduates from the Academy and signs up to join the crew of the newly built Galactica. Much to his disappointment, he is assigned not to a Viper fighter but to a Raptor transport ship named Weasel. He meets his surly co-pilot Coker Fasjovik, who is cynical and interested only in leaving the military, as his tour of duty ends in a month. Coker finds Adama's eagerness irritating. The two are briefed on their first mission together, a routine "milk run" sending cargo to the Scorpia Fleet Shipyards and returning with supplies for the Galactica. It is a four-day trip during which they are to avoid enemy contact of any kind.

While preparing the Weasel for the mission, Adama and Coker find out that their cargo isn't supplies but a civilian software engineer, Dr. Beka Kelly. They depart, but upon leaving Galactica's DRADIS range, Dr. Kelly hands them new orders from the Admiralty. They are to rendezvous with the Archeron, another battlestar, in an area bordering Cylon space. They are also to take all further orders from Dr. Kelly. As they travel to their destination, Dr. Kelly reveals that she worked for Graystone Industries, designing the upgrade for the Cylons' MCP "brain" chip. When they reach the rendezvous point, they discover that the Archeron was ambushed and destroyed. A Cylon raider appears and attacks.

Reeling from the discovery of the ruins of Battlestar Archeron, Adama and Coker’s small Raptor is nearly outmatched when they engage with three enemy Raiders. More secrets are revealed when the crew makes a shocking discovery deep in Cylon space.

Adama and Coker prepare for a dangerous mission above the Cylon occupied planet Djerba. Coker reunites with an old friend and reveals startling news.

Adama dogfights Raiders while the Battlestar Osiris tries to hold off a Cylon Basestar.

Adama, Coker and Dr. Kelly trek abandon the Weasel and trek through Djerba's harsh wind and snow, following a signal with Dr. Kelly's communicator. They track the signal to a huge cave, where they discover their escort unit dead from mysterious non-artillery wounds. Suddenly the cave floor collapses and plunges them into a dark underground chamber. Strange noises surround them and a large snake-like creature lunges out and bites Coker. As Coker struggles to contain the monster, a man rappels into the chamber and kills the snake. He introduces himself as Toth, the only surviving escort. He explains that the snakes, which killed his unit, were created by Cylons doing half animal/half machine experiments. Toth has been alone in the cave for some time and is slightly mentally unstable, prone to unpredictable aggressive outbursts. Nevertheless, he has scouted a route to Dr. Kelly's objective. They leave the cave and stop at a cliff overlooking a seemingly abandoned resort compound.

Waylaid by a ferocious storm, Adama, Coker and Becca reluctantly follow their eccentric savior, marine recon sergeant Xander Toth, to shelter in an abandoned ski lodge. Adama and Coker finally find some common ground and secrets about Becca’s mysterious mission are revealed.

The tentative safety of the ski lodge is abruptly shattered as Cylons breach Toth’s defenses. With Becca and Toth nowhere to be found, Adama and Coker face off against their deadly robotic pursuers. Becca makes a horrifying discovery about the Cylons’ agenda on Djerba.

In the aftermath of the deadly Cylon ambush, Coker threatens Becca, forcing Adama to a heated standoff.

Becca discovers a startling new development that will affect the future of the human race. Meanwhile, Coker’s life hangs in the balance as the team holds out hope for a rescue, and Adama has a disheartening realization about the war effort and his place in it.