On the Galactica, movement inside a cargo container draws the suspicion of Tyrol and his deck crew. When the box is opened, a stowaway is found inside, a pregnant 17-year-old girl named Rya Kibby. Once in custody, she asks to be brought to Doc Cottle.
Meanwhile, a pair of Raptors from the Pegasus, out on a training exercise in a region of intense radiation that interferes with communications, relay a garbled distress signal back to the Pegasus, under the command of the recently promoted engine room chief, Commander Barry Garner. Before Garner and his crew can verify the Raptors' transmission, the Raptors jump away and vanish from the fleet's DRADIS screens.
Ratcheting up the tension aboard the Pegasus is the running feud between Garner and flight training supervisor Capt. Kara "Starbuck" Thrace, a battle of wills that is only made worse by the arrival of Garner's interim XO — Lee "Apollo" Adama, newly promoted to the rank of major.
Back on the Galactica, Rya Kibby's desire to exercise her legal right to an abortion, and the revelation that Doc Cottle has been providing this service to women in the fleet for the past few months, becomes an incendiary political issue. The fleet's pro-life Gemenon faction threatens to pull its support for President Laura Roslin unless she condemns the practice of abortion and makes it illegal.
Aboard the Pegasus, Commander Garner proves unequal to the responsibility of commanding a Battlestar. He insists on mounting a quixotic rescue mission, despite Starbuck's insistence that the signal the Raptors followed was almost certainly a Cylon trap. But when Garner disobeys a direct order from Admiral Adama and orders the Pegasus to go after its missing aircraft, it's up to Apollo to take action and prevent the Pegasus and her crew from becoming the Cylons' next victims. Ultimately Commander Garner's engineering expertise pays off but at the loss of his own life. Admiral Adama, realizing his mistake in choosing Garner, selects a new commander of the Pegasus, his own son Lee.
As the abortion debate flares throughout the fleet, Roslin is forced to take a stand on the issue. Recognizing that every potential life counts in a shrinking human population, Roslin ponders an executive order that will create a wedge issue — one which Gaius Baltar is almost certain to exploit as he launches his own surprise bid for the Colonial presidency.