When Liz begins to undergo some strange, alien-like changes to her body, she decides she needs to get as far from Max as she can. In order to separate from him she must leave Roswell to go to boarding school in Vermont. Meanwhile, Maria gets offered a recording contract in New York, but she isn't sure she likes what the record label people are doing to her music to make it "popular".
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.