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Meier warns Zarek of an unknown spacecraft approaching the Astral Queen while they and other ships of Roslin's faction orbit Kobol in search of the whereabouts of Earth. Meier suggests engaging it using the Adriatic's weapons, one of the few civilian ships of the fleet that had defensive ability. Laura Roslin delays the attack until Kara Thrace identifies herself as piloting the craft.
Later, Meier and Zarek decides that the only way for Zarek to gain access to Roslin's inner circle (and later, with Roslin's death from illness, to rise to power) was for her most influential advisor, Lee Adama, to die. As it was said in the Sacred Scrolls that humans returning to Kobol face a deadly risk, Meier decides that this would be the perfect cover for Adama's death (Home, Part I).
Meier ignores Zarek's order, continuing his plan by recruiting the future Sharon Agathon neé Valerii to assassinate Lee for them, leaving Zarek's hands effectively clean. Meier plays on Valerii's emotional state by telling her of Boomer's murder by Cally, and "warns" her of the same fate from the Adamas. Valerii tells Meier that when they reached the Tomb of Athena, she would "take the father" while he "[took] the son".
At the Tomb's entrance, Valerii draws a Stallion pistol on Adama, prompting Lee to point his pistol at her and Meier to point his weapon at Lee. Valerri double-crosses Meier by turning and shooting him instead, then turning the pistol over to Adama, indicating that the pistol was given to her by Meier. A second, identical pistol falls from Meier's hand as he falls to the ground.
Zarek comforts his friend until he succumbs from the gunshot wound moments later (Home, Part II).