The fleet's exodus has not been clean and easy. After every jump, the Cylons appear exactly 33 minutes later to send them on the run again. Working with little to no sleep, everyone is being pushed to their limit. Baltar himself is put into stress when someone from the Olympic Carrier claims to have evidence he fears could link him to the Cylons' successful attack on the Twelve Colonies.

An act of sabotage leaves Galactica with a 60% loss of its water reserve. The belief that it is an act of a Cylon agent is high among those in the know. Even worse is that Boomer suspects herself to be the saboteur.

With water now found on a nearby moon in the form of ice, a labour source must be used to mine it. The answer is to use the prisoners aboard the Astral Queen. However, convicted terrorist Tom Zarek acts as their leader and organises a revolt, taking hostages with the demand of President Roslin's resignation.

When an accident kills several Viper pilots, Adama puts Kara in charge of training more pilots. But the entire process is troubling for her as she is haunted by memories of Zak.

Moore explained on his blog that the number 33 had no hidden meaning or significance, only that he felt it sufficiently long to allow minor functions like snacking, showering, or cat napping, but was too short to allow anybody to gain any meaningful sleep and recharge their batteries. Further, Moore intentionally gave the number no meaning to avoid creating and inserting unnecessary technobabble into a drama-driven episode.[6]

When a copy of a known Cylon agent boards Galactica and carries out a suicide bombing, the knowledge of the Cylons' new human appearance is shed to the fleet. With the ship's munitions used in the attack, Commander Adama initiates a tribunal to investage the security lapse.

When the Number Six haunting his head suddenly disappears, Baltar finds himself facing a flesh-and-blood copy calling herself Shelly Godfrey who accuses him of collaborating with the Cylons. With evidence at hand, Baltar is madly driven to relieve himself of the charge of treason.

When a Cylon agent is found aboard a ship in the fleet, Adama, by Roslin's request, sends Kara to interrogate the one called Leoben Conoy. Though she approaches impentrable to his tactics, the Cylon engages her in a discussion of his specific dogma, including how special he believes Kara to be.

With Baltar's Cylon detector now operational, Roslin wants Adama to be the one to go first. Adama himself has been acting odd lately, due to his discovery of Tigh's wife, Ellen. The tackling of suspicion between the President, Commander, Colonel and his wife puts Baltar in the middle with the painstaking chore of the screening process.

With fuel running low, and the fleet's only supply occupied by Cylons, Adama plans a dangerous attack in order to obtain the tylium that could last them years. Unbeknownst to those plotting and fighting the battle, divine hands maybe orchestrating things via Roslin and Baltar.

President Roslin uses the arrival of Colonial Day to form a new Quorum of Twelve. But soon Sagittaron's elected delegate Tom Zarek proposes that a vice president be chosen, his popularity quickly earning him a nomination. Not wanting to play into whatever Zarek maybe plotting, Roslin is adamant to choose her own candidate.

A habitable planet is found during a scouting mission. This world turns out to be Kobol, the legendary home of the gods, and its discovery gives Roslin certainty that she is following an ancient prophesy, a belief that threatens to create dividing lines.

By Roslin's request, Kara has jumped to Caprica to retrieve the Arrow of Apollo where she encounters a familar face and a startling revelation. Following Kara's defiance of his orders, Adama has more betrayals waiting for him - one coming from the most unexpected person.