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.
After escaping from Pierce, the aliens save Nasedo. Michael accidentally kills Pierce. Nasedo, as the aliens' guardian takes Pierce's place to help the aliens. The aliens figure out how to use the devices and release a message from Max and Isabel's real mother. She says Max is their leader and Tess, his fiance and that Michael is Second in command and he is Isabel's fiance. After hearing all this Liz runs out.
The Skins make all the humans in Roswell, New Mexico disappear turning it into a ghost town. Their assault ends with the death of one of the aliens: Courtney the helpful Skin. Fortunately Tess uses her mindblowing powers and destroys all the other Skins or so it seems until Max and Tess spy a boy resembling Nicholas on a scooter at the end of the episode.
Max and Tess depart for the interstellar summit in New York City with Rath and Lonnie, Michael and Isabel's duplicates, who both harbor a secret agenda for their future king and an alliance with Nicholas, the Skin. Ava reveals to Liz that Rath & Lonnie murdered Zan. Tess is kidnapped by the dupes after Max learns of their true intentions. When Max finally finds Tess she reveals that they tried to read her mind to find the Granolith but she resisted. She then says that they're gone but did they die or are they still out there? Ava says goodbye to Liz and leaves Roswell.
Max witnesses a tragedy and is haunted by the ghost of a man he could have saved, leaving him overwhelmed with guilt and questioning his healing abilities. Isabel aka the Christmas Nazi (dubbed by Michael) tries to brighten up the holiday season and Tess tries to became a part of the Valenti family.
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.
A startling breakthrough leads to a renewed connection for two of the gang. Differing reactions to a life shattering event creates tension among the gang, resulting in heartfelt revelations, hidden insecurities and thoughts of leaving Roswell. Meanwhile, Liz enlists Sean in her continuing quest for answers into the death of Alex.
Max is hit with a one-two punch after he discovers that not only is Tess pregnant with his son, but that the baby cannot survive unless they return to their home planet. Liz, Maria and Michael work together to unravel the mysterious double life of Alex. Isabel and Kyle explore her powers as they play pranks on Max and Kyle dreamwalks with a Playmate.
Brody Davis, his mind frazzled from an electric shock,holds several members of the gang hostage, when he begins to remember what happened when he was abducted, such as the New York City interstellar summit and the fact that Max is an alien. Max must use his healing abilities to fix Brody's mind so that he doesn't remember the alien mind that inhabits him. Tess must mindwarp Amy DeLuca into not remembering that Brody held them hostage.
With Alex's ghost as her guide, Isabel must finally confront her fears about love and her conflicted feelings for Jesse. Meanwhile, Maria happily discovers a whole new, human part of Michael in, of all places, a bowling alley, and Liz and Max struggle to remain together despite her father's insistent disapproval.
Max travels to Hollywood while investigating a murder he believes was committed by an alien. He discovers a link to a Paramount science fiction show called "They Are Among Us" and when he goes to the Paramount lot to investigate he ends up auditioning for the part of an alien on an episode of "Enterprise" directed by Star Trek alum, Jonathan Frakes. Meanwhile, back in Roswell, Isabel and Jesse struggle over how to reveal their engagement to their families.
After their idyllic wedding, Isabel and Jesse are stalked on their honeymoon by her alien lover Kivar who plots to take her back to their home planet. Learning of this, Max and Michael arrive intent on destroying the alien. Meanwhile, Liz and Maria discover that Philip has begun a secret investigation of Max, including the diappearance of Tess, and he's embroiling Liz's dad into the whole thing.
When a journalist friend of Jesse's comes to Roswell, Isabel discovers he's investigating her, Max and Michael, after he witnesses Michael using his powers. Meanwhile, Isabel fantasizes about what her life would be like if Jesse knew her alien secret through the device of a 1960s sitcom a la "Bewitched."
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."
Michael uncovers a conspiracy at Metachem, when a guard is killed on duty. Michael enlists the aid of Max and Isabel when the investigation takes an alien turn. Meanwhile, Liz has entered boarding school in Vermont and tries to start a new life, and Maria disillusioned by New York goes to visit Liz in Vermont.
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.
Michael witnesses a fatal crash between a fighter jet and an alien vessel, and embarks on his own investigation leading to the recovery of an artifact. Meanwhile, Isabel spends the day with her mother, who's harboring a secret agenda and is working with her husband to discover Max & Isabel's secret, which leads to a shocking revelation.
Max's quest to find his son ends with the return of Tess and the baby, and the gang find themselves in danger again while trying to protect the child. Meanwhile, Jesse encourages Isabel to reveal her true origins to her parents, and the elder Evanses provide a way to ensure their grandchild's safety.
As their high school graduation approaches, the gang must come to terms with their expectations for the future, while joining together to thwart the FBI when they discover that several members of the group are under surveillance. Meanwhile, Liz begins exhibiting even more alien-like powers, that cause her to see visions of their future - including their deaths.