The survivor count shown in the title sequence is 39,674.
The episode continues from the previous episode "Guess What's Coming to Dinner?" with the mortally injured Cylon Natalie being taken to the sickbay. After seeing visions of green trees, she dies. President Laura Roslin visits the Basestar accompanied by half of the pilots. After the hybrid is plugged in, the Basestar immediately jumps away to unknown coordinates. The Quorum must find a replacement for Roslin, who is assumed kidnapped. The Quorum can elect a temporary president, so Lee Adama solicits the help of a reluctant Romo Lampkin in choosing the best candidate.
Admiral Adama questions Lt. Sharon "Athena" Agathon in his quarters regarding why she shot Natalie. Athena confesses to Adama about the visions she had of Natalie and Gaius Baltar taking away her half-human, half-Cylon child, Hera. She is sent to the brig.
Admiral Adama must now both protect the fleet and find the rebel Basestar with Roslin and his troops on board. He orders Colonel Saul Tigh to interrogate Caprica-Six in the brig to try to get information from her about the Cylon hub. Tigh's interrogation/liaison is interrupted when a badly damaged missing Raptor jumps into contact range. The raptor's flight data recorder shows where its jump had originated. A raptor scouting mission to those coordinates finds the remains of a battle with a destroyed Cylon Basestar, Viper and what is assumed to be the hub. Adama does not believe the destroyed Basestar was the rebels' ship with Roslin on board, and he orders 4 raptors to remain there in case it returns.
Admiral Adama meets with Colonel Tigh in his cabin and confronts him with the information that he knows about Tigh's “meetings” with Caprica-Six in the brig with the cameras turned off. Adama reveals to Tigh that Caprica-Six is pregnant. Tigh, in shock, does not deny that he is the father; Adama accuses him of betrayal. Tigh in turn accuses Adama of risking the whole fleet by searching for Roslin. Angers explode and a short but brutal fight ensues between the two men, but the old friends soon stop and accept their unusual emotional predicaments.
All the names on the list of potential presidential candidates have been eliminated, but Lampkin realizes that there is only one name who could possibly replace Roslin even if it was not on the list. After finding Lee, Romo congratulates him on his successful candidacy, but Lee explains he was never a candidate. Lampkin does not listen and pulls a gun on him. Lampkin is distraught because he lost his wife during the attack on the colonies and does not believe humanity deserves to have a president who gives such hope as Lee would. Lee Adama convinces Lampkin that there is hope and that he will make a difference. Lee is sworn in as acting President.
Admiral Adama will no longer risk his remaining pilots or the fleet in looking for Roslin, and hands over command of the Galactica to Tigh. The Admiral takes a Raptor and remains behind. While he waits, he reads the charred copy of Searider Falcon which was recovered from the damaged Raptor.
This is a Latin phrase meaning "without which nothing", describing the absolute essence, the integral element of a situation or process.