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Veronica is hired by Bonnie, a promiscuous classmate, to find out who secretly slipped her the morning after pill, causing her to have a miscarriage. The investigation leads her to the office of Bonnie's boyfriend, Tim Foyle, and while searching his computer, Veronica discovers Tim has uncovered a witness to Dean O'Dell's death. Together, Keith and Veronica visit Bonnie's father, a well-known televangelist, Reverend Capistrano.
Veronica confronts Logan about sleeping with Madison Sinclair while they were broken up.
There's Got to Be a Morning After Pill puns on the title of Maureen McGovern's 1971 pop song, "There's Got To Be A Morning After" which played over the end credits of the 1972 disaster film The Poseidon Adventure. The A-plot in this episode turned in the covert administration of the drug mifepristone, or RU-486, an emergency contraceptive commonly referred to as "The Morning After Pill." Mifepristone may also be used to induce early abortions, as happened in this episode.