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The Peace Conference
In the course of destroying some scout Raiders that approach, Zac's Viper loses power to one engine. After the Raider fleet begins their run towards the peace conference and the battlestar fleet, Zac tells his brother to go ahead to warn the fleet, allowing Apollo to report the enemy activity back to Galactica. Apollo is able to warn Adama, but Zac is killed by the Raiders as they caught up with the disabled Viper just as Zac entered visual range of the Colonial fleet (Saga of a Star World).
When Adama insists on going to the surface of Caprica in a shuttle, Apollo insists that the commander ride to the planet as a passenger in his Viper for added protection. On the surface, Apollo is accosted by angry colonists who survived the genocide, but Adama is able to rally them to find any ship they could fly to leave Caprica and to Galactica's protection.
After the Cylon Attack
Apollo helps inspect ships in the newly formed fleet. While aboard the freighter Gemini, he discovers that certain individuals were hoarding supplies aboard the Rising Star, while others went without. Apollo ensures that supplies are fairly distributed, much to the displeasure of Sire Uri. Apollo encounters Serina, and helps her cheer up her son (Boxey) who is depressed.
In front of the Quorum of Twelve, Apollo suggests the Straits of Madagon as a possible route to Carillon, volunteering himself as well as Boomer and Starbuck to help clear the minefield. The minesweeping operation earns the three a Gold Cluster.
On Carillon, Apollo gets to know Boxey and Serina better. Apollo and Starbuck save Boxey, Muffit, and Cassiopeia from the Ovions, while lighting a fire in the tylium mines. The pair use a clever bit of deception to force a Cylon basestar into the atmosphere as the tylium fires destroy the planet and the nearby basestar (Saga of a Star World).
Apollo and Serina announce their intentions to be sealed. Apollo and Starbuck discover a magnetic void while on patrol. Their mission prevents them from catching the mysterious illness that affects the rest of the Viper pilots. Apollo trains female shuttle pilots, including Serina, to be Viper pilots. Apollo leads the new pilots on a successful raid against an outpost before the Fleet turns and heads into the magnetic void (Lost Planet of the Gods, Part I).
Apollo and Serina chase after Starbuck, who leaves on a mission without them. Starbuck is captured by the Cylons, but Serina asks to go ahead with the ceremony. Apollo and Serina join an expedition to Kobol, and follow Adama into the Tomb of the Ninth Lord of Kobol. Baltar arrives and accidentally triggers a trap, sealing all four into the tomb. A blast from a Raider frees them, but as they escape Serina is shot by a nearby Centurion. The mortally wounded Serina is brought back aboard Galactica where she says goodbye to Apollo and Boxey (Lost Planet of the Gods, Part II).
While decoying Cylons away from the Fleet, Apollo's Viper runs out of fuel, causing him to crash-land on Equellus, a low-tech planet far removed from the Fleet's flight path. Marooned within an agrarian community, he befriends Vella and her son Puppis, joining with them in the fight against strong-arm man Lacerta. Apollo destroys Lacerta's right-hand "man", Red-Eye, a marooned Centurion with memory problems, ending Lacerta's reign of terror. Despite his new love with Vella, Apollo returns to the Fleet when Vella shows him another crashed Viper containing the needed fuel (The Lost Warrior).
Apollo and Boomer rescue Starbuck from the Proteus prison and return his lost recon Viper. All three of them manage to eliminate the Raiders that had been dispatched to investigate, and return to Galactica safely.
Apollo is chosen to lead the mission to Arcta to destroy the Ravashol pulsar. He is dismayed when he finds Boxey has stowed away on the snowram (The Gun on Ice Planet Zero, Part I). His team successfully destroys the pulsar, ensuring the survival of the Fleet (The Gun on Ice Planet Zero, Part II).
Apollo, accompanied by Boomer, pilots the shuttle that rescues Starbuck, stranded on the planet Antilla. Apollo wisely suggests the use of a shuttlecraft, rather than a Viper squadron, so as not to attract Cylon attention (The Young Lords).
Apollo and Starbuck encounter the battlestar Pegasus while on patrol. With the two battlestars reunited, Apollo takes part in a joint mission to capture the Cylon tankers, which fails due to Commander Cain's sabotage (The Living Legend, Part I). Apollo leads the commando team that parachutes down to Gamoray to destroy the command center of the planetary defense systems. After the command center is destroyed, the duo join the fight above the planet. Apollo and Starbuck break from their assigned escort duty to help Pegasus defeat two Cylon basestars (The Living Legend, Part II).
When Galactica is severely damaged by suicidal Cylon Raiders, Apollo hatches the idea of modifying Vipers to shoot fire-extinguishing boroton into the burning landing bay. When that fails to completely put out the flames, Apollo and Starbuck undertake a risky spacewalk to plant explosives on parts of Galactica's hull. This successfully vents the fires into space. While on the spacewalk, Apollo has the idea of placing mushies next to the ventilation duct on the bridge to lure Muffit through the convoluted maze of ducts. The idea works, saving the lives of Boomer, Athena, Boxey, and numerous other crewmembers stranded in the rejuvenation center (Fire in Space).
Apollo's team discovers Count Iblis. Apollo is wary of Iblis, especially due to the apparent threat against Adama's power (War of the Gods, Part I). Apollo later confronts Iblis, and ends up stepping in front of a blow meant for Sheba. Apollo is killed, but by doing so Iblis apparently oversteps his bounds and is forced to flee. Apollo is resurrected by the Beings of Light, and returns to Galactica with Sheba and Starbuck (War of the Gods, Part II).
Apollo accompanies Starbuck to the Rising Star, where Starbuck plans to try a new Pyramid system. They discover Chameleon, and inadvertantly protect him from the Borellian Nomen that are pursuing him (The Man with Nine Lives).
Apollo and Boomer serve as Starbuck's "Protectors" (legal council) when he is framed for the murder of a Colonial warrior. Apollo manages to get the real killer to reveal his entire plot while Boomer pipes in the audio so that the Tribunal can hear the confession (Murder on the Rising Star).
Apollo helps the Terrans Sarah Fowler, Michael, and their children reach Paradeen. Once on Paradeen, Sarah sabotages the Vipers in hopes that Apollo will stay and be with her. She eventually warms up to Michael, and Apollo helps to capture the Eastern Alliance soldiers that show up (Greetings from Earth).
While out on patrol, Apollo is taken aboard a Ship of Lights. There, John recruits him to help the Terrans. Apollo poses as a Terran Nationalist to try to avert a war. With some help from Starbuck, Galactica ends up protecting the Nationalists from the Eastern Alliance missiles. Their attack thwarted, the Eastern Alliance is forced to consider peace as an option (Experiment in Terra).
When Starbuck visits an old flame aboard the electronics ship, Apollo accompanies him. Shortly after they arrive, they find Aurora apparently involved in an ill-fated mutiny attempt. They accompany the senior officer with the prisoners, taking a shuttle to Galactica for trial. The first officer has other plans, and attempts to strand their shuttle. With the help of the prisoners, the group manages to return to the electronics ship. They suprise the crew, and retake control of the Celestra (Take the Celestra).
Apollo takes Starbuck, Cassiopeia, and Sheba up to the Celestial chamber. Inside, they discover an Gamma frequency old signal. With Boomer's help they trace the direction of the signal. Scouting in that direction, they discover a Cylon basestar, but manage to flee before being detected. Adama decides to engage the basestar. Apollo hatches a plan to use Baltar's raider to infiltrate the basestar and knock out its sensors. Apollo and Starbuck succeed in the mission, and Galactica destroys the basestar (The Hand of God).
Changes in the Proposed Second Season
In Glen Larson's proposal for the Original Series' second year, Apollo would "gingerly [begin]" to pursue a relationship with Sheba, as implied at the end of "The Hand of God". However, this relationship would end tragically by her death in a battle with the Cylons, a death that could have been avoided had he heeded Starbuck's objection, which comes from a "sixth sense" he has about bad happenings.
After her death, Apollo has an epiphany where he decides to step down from command of Blue Squadron, telling his father that he will not be responsible for another man. Adama respects the decision, although he does not agree with it, and Apollo begins a hedonistic approach to life that "even has the fun-loving Starbuck envious". After running into Pegasus, Apollo falls in love with the ship's new executive officer, Renata. However, despite his infatuation with her, he discovers that she is a new breed of Cylon that is half-human, half-machine, and thwarts her plans to take over Pegasus's remaining crew (The Return of the Pegasus).
Apollo later finds himself at odds with his sister, Athena, who leads an insurrection against the "male dominance" of the Fleet. After a woman straps a bomb on herself, threatening to destroy Core Command, Apollo manages to talk sense into his sister, who in turn talks the potential suicide bomber down (A Woman's Power).
Later, as Apollo and Starbuck continue to develop their "Butch Cassidy and Sundance Kid" relationship, Apollo comes across a planetoid that is a veritable paradise. On this planetoid, Apollo falls in love with its princess, Quoi-Ling, despite the objections of her scheming brother, Prince Choi-Ling. Apollo, Starbuck, and Quoi-Ling manage to leave the planetoid, however this act cost Quoi-Ling her life, since she rapidly ages upon leaving the planetoid (Island in the Sky).