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Baltar kills Delegate Michael Tigh after the Quorum's decision to immolate Pythia for her crimes of herecy, which prompts a conflict between members of the polytheistic Twelve Tribes and the atheistic Thirteenth. After Tigh is resurrected, Baltar continues plotting his attacks on the Thirteenth by destroying the local resurrection facility and attempts to kill Tigh a second time. Tigh, however, escapes death by wounding Baltar instead—but Baltar kills Pythia, who is human and so cannot be resurrected (Battlestar Galactica: The Final Five 1).
Baltar stows away aboard the Resurrection Ship in the Thirteenth Tribe fleet that leaves Kobol, and sets off an explosion which causes the ship to crash on the Algae planet. He is overcome with remorse when he sees the resultant devastation and the grieving Cylons, however. Baltar and Tigh have another confrontation, which is broken up by the return of Pythia from the dead. Pythia sends Baltar back to the twelve tribes of Kobol with the Book of Pythia (Battlestar Galactica: The Final Five 2).