Liz tries to maintain her relationship with Kyle despite her deep bond with Max; Michael is obsessed with the idea that there was another alien in Roswell in 1959 and tries to decipher the meaning of the flashes only he sees. Meanwhile, Liz suspects the new guidance counselor Ms. Topolsky is hiding something, especially when she sees her with Michael's file.
Max, Isabel and Michael have been hiding a secret for their entire lives - that they come from a different planet. When Max is exposed while saving Liz's life, a girl who attends their high school, it eventually leads to a few others learning their secret. The three aliens and their new friends try to go about their normal lives while trying to discover more about where they come from and how to get home - all while keeping their identities secret from the rest of the world.