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When Galactica provides protection for a asteroid mining operation, Clellan is among those taking part in regular picket patrols of the area. He is also present during marksmanship training for Viper nugget Joseph "Jo-Jo" Clark, commenting that his first attempt at the same training faired worse than Clark's.
During a patrol of the Big Spud, Clellan unsuccessfully calls for Brent "BB" Baxton to retreat when their Vipers become on low fuel. Baxton, a nugget, ignores orders and engages a group of Raiders with fatal results. Additionally, Clellan helps account for Reilly's belongings after the pilot is killed by Scar and he is later present in the pilot's rec room when Kara Thrace toasts to the deceased pilots (Scar).
When a colony on New Caprica is established, both Clellan and Nora muster out of Colonial fleet service as she wants to settle down and have a family. He is approached by Galen Tyrol and James Lyman to join the resistance efforts when New Caprica is occupied by Cylons, but declines over the desire to be a husband to Nora.
Following Nora's death in a Cylon attack on a temple, Clellan becomes violently upset at the revelation that the resistance was hiding weapons there. After a brief period of mourning, he relents and agrees to join the insurgents. His first assignment as a resistance member involves infiltrating the New Caprica Police, where he keeps an eye on both the Cylons and their human collaborators (Battlestar Galactica: The Resistance).
He later agrees to become a suicide bomber when the resistance learns about an NCP graduation ceremony, believing that Gaius Baltar will also be present. When Samuel Anders asks whether Clellan is committed, Clellan replies that, without Nora, he has nothing left to live for.
Despite Baltar's last-minute withdrawal from the ceremony, Clellan detonates his bomb, killing 33 people and several Cylons in the process ("Occupation", "Crossroads, Part I"). Subsequently, the Cylons begin a crackdown on all individuals thought to be resistance members. They orchestrate mass abductions and executions of suspected insurgents; surviving NCP members, lead by his former friend, Lyman, carry them out ("Precipice", "Exodus, Part I", "Exodus, Part II").
Later on Galactica, Lee Adama and Kara Thrace make a pact about where to place each other's photos on the wall of memories should either die. Adama requests to have his photo placed next to Duck and Nora, commenting: "Good card players. Nice way to spend eternity." (Maelstrom)