With President Roslin and Apollo in the brig and Commander Adama still recovering from surgery, Colonel Tigh is faced with explaining the situation to an angry Quorum of representatives who want to know where their President and Commander are.
Hiriam Boyd (Tauron), Walter Bagot (Virgon), Sarah Porter (Gemenon) and Tom Zarek (Sagitaron) confront Tigh about removing the President from office, reminding him that the military has no authority to do so under the Articles. Zarek accuses Adama of trying to pave the way to instate martial law and bring a military dictatorship to power. Colonel Tigh defends Adama's decision, but the Quorum takes a vote, motioning that they be allowed access to their incarcerated President. All twelve vote in favour and Tigh is forced to submit.
At some point, a mission organised by Colonel Tigh to retrieve supplies from the transport ship Gideon goes horribly wrong. Tigh sent Joe "Hammerhead" Palladino on the mission, but the reality of the situation was that Apollo should have been in charge - he was in the Brig. As they tried to load the supplies from the Gideon, the civilians onboard got very angry and saw it as a kind of invasion of their ship. After they got violent, some of the marines lost their nerve and shots were fired, killing 4 civilians and injuring many more.
While in the Brig, Apollo had been timing the movements of the guards, evidently planning an escape, but later he is released by Colonel Tigh but apparently under heavy guard. After being released, Apollo proceeds to get various crewmen to side with him and forms a plan to break the President out of the Brig. Somewhat later in the episode, the (very scared) President is escorted out of the brig by some crewmen. They make their way to the flight deck where Apollo is waiting for them with two Raptors to take her Kobol. It seems that many crewmen have chosen to go against orders and follow Apollo. They take the President to Kobol, where their scans reveal the Colonial Raptors on the surface...
Meanwhile, Starbuck, Helo and Boomer are still on Caprica. Starbuck and Helo are underfire from two humans (who they believe to be Cylons) - Anders and Sue-Shaun. Similarly, Anders and Sue-Shaun believe Starbuck and Helo to be human-form Cylons. Eventually, they end up in a stand-off trying to convince each other that they are all humans, which they do.
The four travel to a school, where it seems that the other humans on Caprica have some form of base. Anders and Starbuck develop a real friendship (and possibly more), somewhat consolidated by their playing together on the Pyramid court, where Starbuck is beating Anders, despite her injured knee.
Also in this episode, we see Jammer, Bongo and Cally building a "cage", which they are expecting their Chief (Tyrol) to be put in. Jammer and Bongo believe that the Chief is a Cylon, but Cally defends him, saying that Boomer tricked him.
* All spoiler information is subject to change.