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Before the Discovery of the Thirteenth Colony
He accompanies Admiral Helena Cain's delegation to Galactica, and shows off his 48 kill markers to fellow pilots Margaret "Racetrack" Edmondson and Kara "Starbuck" Thrace that earn him scorn from the latter.
Allison is later part of the group of Pegasus alert vipers that launch in response to Galactica's Viper squadron launch. Allison assumes the role of flight leader while their CAG, Cole "Stinger" Taylor, is preparing for the Raptor recon mission.
After Pegasus's destruction, he continues as a Viper pilot on Galactica, participating in the botched training mission that leads to Kara Thrace's removal from flight status by Galactica's CAG, Lee Adama. He is also present when Brendan "Hot Dog" Costanza suggests "Athena" as Sharon Agathon's callsign (Torn).
During a flight briefing, Allison vocally announces the fact the Fleet has gone 49 consecutive days without a Cylon encounter, earning him a witty retort from Thrace regarding his flying skills (A Day in the Life).
Two weeks after Kara Thrace's death, Allison is present during the daily mission brief conducted by Lee "Apollo" Adama, immediately prior to his being taken off flight status and replaced with Karl "Helo" Agathon as CAG (The Son Also Rises).
Post-Thirteenth Colony and the Mutiny
Allison assists Felix Gaeta with his mutiny aboard Galactica by arming a number of civilians with stolen munitions on C-deck. When Kara "Starbuck" Thrace demanding to know why he was in charge, he brusquely tells her to evacuate with the others. After the mutiny is nearly complete, Allison is flying CAP with Brendan "Hot Dog" Costanza when Gaeta orders him to use deadly force to stop the Raptor with Laura Roslin and Gaius Baltar aboard, in order to prevent the Raptor from landing aboard the rebel basestar (The Oath).
After learning that Roslin is aboard the Raptor, Costanza refuses to fire, forcing Allison to launch a missile at the Raptor, which misses its target and hits the baseship. The Raptor makes it to the baseship, and Allison breaks off the attack. He is later assigned command of a firing squad ordered to kill Admiral William Adama, showing some reluctance though he goes through with it. Before the execution can be carried out, Adama is rescued by Lee Adama, Saul Tigh, Karl Agathon, Sharon Agathon and Aaron Kelly; Allison is forced at gunpoint by Tigh to report Adama dead and seems a bit relieved not to have to go through with the execution. Adama convinces the Marines to join him in retaking the ship, however Allison refuses stating that while he highly respects Adama, he hates the Cylons and won't serve under someone who won't fight them; Adama orders him tied up rather than killed as Tigh wants (Blood on the Scales).
After the rebellion is put down, Allison is presumably incarcerated on the Astral Queen with the other mutineers. Weeks later, Admiral Adama offers the mutineers their freedom in exchange for participating in what is almost a suicide mission to rescue Hera Agathon from John Cavil's forces, although Allison's participation in this battle is unknown ("Daybreak, Part I"; "Daybreak, Part II").