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Alan Mooney was the Principal of Neptune High. He was Vice Principal when Lianne Mars was a student. At the time, he has an affair with then-student Mary Mooney and would later learn that she was pregnant. He suspends Lianne and her friend Deborah Hauser for "spreading rumors" (Deborah was the guilty party, but Lianne recanted to protect her scared, pregnant friend). Mary later leaves the baby on his doorstep. He, in turn, left it in the girl's bathroom during the prom to make it look like it was a student's child.
Years later, however, Lianne's own daughter, Veronica Mars, follows up on the story after reading her mother's student file. Veronica discovers that the prom baby was Logan Echolls' half sister, Trina Echolls. She and Trina faked a story about Trina needing bone marrow to try smoke out the mother, believing it to be Celeste Kane. Mary tells Veronica everything, who then passes it on to Trina. Trina then crashes a faculty meeting and abruptly tells everyone in the room that Moorehead is her father and was the one who left her at the prom. Moorehead is subsequently fired and Vice-Principal Van Clemmons takes over. Veronica deduces that it was Clemmons' plan all along to feed Veronica a lead he knew she would follow and expose the truth, ensuring his promotion.