Hero starts out with the fleet encounters two Cylon Raiders in pursuit of a third. Starbuck and Kat take out the two pursuing Raiders and engage the third when a panicked male voice comes over com identifying himself as Lt. Daniel "Bull Dog" Novacek and pleads to call off the attack. Admiral Adama then allows the Raider to land on the Galactica and a disheveled man emerges from the cockpit. Adama welcomes the man aboard apparently knowing who he is. Novacek is checked over by Dr Cottle who confirms he is not a Cylon and in good physical health.
Novacek is then debriefed by Adama who is curious to know how he escaped the Cylons. Novacek jokingly says he grew tired of their poor service and accommodations and decided to leave. Later he explains he was held prisoner for the past three years and found an opportunity for escape when the Cylons showed signs of sickness. Adama believes it was the effect of the virus they found killing the Cylons earlier, to which Novacek says he was apparently immune.
Later in a meeting with President Roslin, she asks for more details on Novacek's situation, where Adama informs her that Novacek was a pilot for the Stealthstar Viper during a black op mission when he was in command of the Battlestar Valkyrie. Adama was sent to the Tauron colony that was violating the Cylon Peace Treaty by mining Tylium on a planet that was too close to the Armistice Zone. Novacek piloted the stealth fighter on a recon mission but the Taurons shot him down. Adama says he didn't know Novacek had survived. After Novacek leaves, Roslin becomes suspicious and asks Adama to tell her what really happened. Adama tells her to "trust" him on this one and he'll handle it.
Elsewhere, the Number Three is wandering the corridors of Galactica dodging security personnel. Once it becomes apparent they are after her she runs away coming upon a door she cannot open which reads "End of Line". She turns to the group of human soldiers telling them to shoot her and they do but she quickly awakens from the dream back aboard a Cylon Basestar and is in bed with Gaius Baltar and Number Six.
Back at the fleet, Adama goes to Tigh's quarters to tell him about the reappearance of Novacek to which Tigh is baffled to how the man had survived his recon mission and wonders what Adama plans to do about it since Novacek's return could cause a situation if the truth is found out.
Later, Adama meets with Lee to discuss Novacek. There Adama tells Lee the truth about the Tauron mission. Adama was ordered by the Colonial Admiralty to conduct surveillance on the Cylons. They thought they could get a stealth ship across the Armistice Zone and infiltrate the Cylons' rebuilding efforts. During the mission, Raiders appeared and disabled Novacek's fighter. Lee is shocked to learn that the military knew the Cylons were using the "Peace Treaty" to strengthen their forces and the inevitable all out attack on the colonies. Adama then tells Lee the worst part of the mission, that it was his decision to shoot down Novacek himself to avoid his being captured. He feared that if the Cylons captured him, they would retaliate knowing the humans violated the "Peace Treaty" first by spying on them. At the same time, Novacek has paid Tigh a visit, where Tigh accidentally reveals the truth about the mission to him as well, thinking Novacek already knew what really happened. Meanwhile, Adama continues with the story, lamenting that the failed mission was probably what instigated the Cylon attack that nearly wiped out the entire human race. Despite protests from Lee, Adama believes that he is responsible for the entire situation the human race is now in.
Back on the Basestar, Number Three's dreams grow increasingly worse and she seeks release. She orders a Centurion to kill her, overriding its directives and telling it to delete the incident from its memory afterwards. The Centurion promptly shoots her in the head and she is resurrected. After awakening from her death, she tells a Six that the state she enters during the transition of her download is "so beautiful," apparently getting a rush from the effect to temporarily escape her mental torment.
Back on board Galactica, Starbuck analyzes the gun camera footage of the Cylon Raider chase of Novacek and finds something curious. She brings hard copies of the images to Tigh where she says the Raiders had every opportunity to shoot Novacek down but it looks like they were purposely missing their target. She is also skeptical about Novacek not only escaping the Cylons, but how he just happened to find the fleet as well. Tigh becomes concerned and goes to inform Adama.
Adama is in his quarters when he gets an urgent call from Novacek asking to talk to him. Adama quickly heads down entering Novacek's quarters where Novacek strikes him in the stomach with a metal pipe. Adama stoops over and Novacek clocks him in the face sending Adama crashing into a table. Novacek ties Adama up and begins choking him, furiously blaming his former commander for sending him on a mission to be captured and tortured by the Cylons for the past three years.
Tigh comes to Adama's rescue pointing a gun to Novacek's head and demands he stand down. Novacek goes for Tigh's gun but Tigh shoves him off and whacks the gun from his hand with the pipe. Tigh tells Novacek that he was duped by the Cylons. They purposely let him go and drove him toward the fleet, somehow knowing that he'd try and kill Admiral Adama. Novacek finally comes to his senses realizing he was just doing the Cylons' dirty work for them.
A while later, Adama goes to Colonial One and hands his resignation to Roslin saying he has to face up to what he has done and no longer deserves his command. Roslin refuses his resignation as she was just about to award him with a medal of distinction for his 45 years of service in the Colonial Military. Adama says he doesn't deserve it, but she admits the medal is not for "him" but for "them," the men and women under his command. When Adama laments his role in destroying the human race, Roslin responds by saying that the matter was both anybody's and everybody's fault. His penance in the Novacek matter will be to accept the medal, like it or not, and continue his job.
Adama accepts his medal of distinction and after the ceremony he sees Novacek off as he departs for another ship in the fleet and attempts to rebuild his life as a civilian. Before he departs, Adama shakes hands with him and gives him his Fleet uniform, reminding him "once a pilot, always a pilot," and the two salute each other one final time. Adama is later paid a visit in his quarters by Colonel Tigh, who is uncertain as to why he went to Adama's quarters in the first place. When Tigh rebuffs Adama's plea for him to return to his duties as the Galactica's XO, Adama then asks him if he's ready to talk about what happened to Ellen. Tigh says he needs a drink to which Adama replies, "Me too." The two sit down to talk as the episode ends.