Michael discovers the hidden history behind the 1947 crash when interviewing a World War II survivor for a school project. The story unfolds with familiar faces portraying people in 1947.

The Skins make all the humans in Roswell, New Mexico disappear turning it into a ghost town.

Sheriff Valenti is suspended from the force after refusing to answer the FBI's questions about Max and Isabel, but he soon finds himself right back in the thick of things when Laurie DuPree shows up at his house claiming to be chased by aliens.

Max tries to stop Alex and Kyle from being buried alive in a cave filled with glowing blue crystals; Isabel is kidnapped by Grant Sorenson possessed by the alien parasite queen; Michael is shot while trying to protect Laurie.

When the gang makes a spur-of-the-moment trip to Las Vegas, in order to spend the DuPree money, the event-filled excursion ends in a faceoff between Max and Michael over leadership; Tess and Liz can't pass for over-21-year-olds; Maria recruits Alex to help her audition for a role that ends up to be for a stripper; Isabel meets a man.

Liz continues her investigation into Alex's death while Isabel plans her future and Maria wonders whether Michael will always be around.

Max, with the help of Kal Langley, undertakes a dangerous journey as he seeks to learn of the fate of Tess and his son. Meanwhile, back in Roswell, Isabel and Jesse must face the negative reactions of their parents and friends to their impending marriage.

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."

When the gang attempts to return to their normal lives, they soon find that their lives have gotten a lot more complicated, which includes Jesse attempting to come to terms with his newfound knowledge but matters are complicated when he finds himself under FBI scrutiny, and Max's "death" creates a unique situation within the alien authority structure, resulting in a new King...Michael.