Apollo, freshly promoted to Major, is assigned to the Battlestar Pegasus to assist her new captain, Commander Barry Garner, the ship's former senior engineer. When two Pegasus Raptors sent out on a routine training mission by Captain Starbuck disappear from DRADIS, Commander Garner places all blame on Starbuck, implying that she is negligent.
On Galactica, a pregnant teen stowaway is discovered who seeks an abortion by Dr. Cottle. She requests political asylum while her Geminese family demands that she be returned to them. When the issue is brought to President Roslin, she initially embraces the legality of abortion prior to the Cylon attack, but is pressured by the representative of Gemenon - an important constituency for Roslin's run for reelection. When discussing this with Admiral Adama, he points out the need of babies for the survival of the human race. Vice President Baltar provides a calculation that at the current rate humanity will become extinct in 18 years.
On Pegasus, Starbuck concludes that the missing raptors may have jumped away to answer a phony distress call, a common Cylon tactic. In light of the danger, Admiral Adama orders a cautious recon mission to find the missing ships. Commander Garner, discounting Starbuck's theory, jumps the Pegasus to the location where they find the missing crews dead and are attacked by three Cylon Basestars. With the FTL drive damaged, Garner places Apollo in command of the ship and rushes to repair the FTL drive.
Apollo is able to fend off the attacking Basestars and buy time for Garner's engineering. Garner succeeds in repairing the FTL drive but dies in the process. Apollo jumps the Pegasus back to safety and is rewarded by his father by being promoted and appointed Commander of the Pegasus.
Back on Galactica, President Roslin issues an executive decree banning abortion but not before allowing the Gemenese girl to terminate her pregnancy and granting her asylum, thereby infuriating the Gemenese representative. During a press conference, Vice President Baltar publicly denounces Roslin's decision and announces his candidacy in the upcoming elections