Bizarre things start happening in the little New Mexico town where UFOs were spotted in 1947. Cut to 1999, when a cute high-school student saves the life of a teenage waitress. Surrounded by cliques of clever, angst-filled classmates, the two form a bond that threatens the survival of a secret universe involving superhuman powers, a yen for hot sauce and an alien gene pool.
Max and Liz are arrested and jailed for holding up a convenience store. Meanwhile, Isabel has a secret affair with a handsome attorney, and Michael tries to straighten out his life.
Michael works as a security guard, but when he tries to loosen up his co-workers, he causes more harm than good. Meanwhile, Max and Liz continue to see each other despite her parents' wishes.
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.
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.
Right before her wedding, Isabel is torn with doubt when she has erotic dreams of her former alien lover, Kivar. Meanwhile, a reluctant Max agrees to serve as Jesse's best man, while attempting to investigate him at the bachelor party.
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 an old love visits Maria her passion for music resurfaces, which jeopardizes her relationship with Michael. Meanwhile, while Max's father is still trying to put together all the pieces of his investigation, Isabel joins Max in the quest to stop him.
When Max is fascinated by an intriguing autistic child he wonders if his own lost child is attempting to reach out to him. Meanwhile, Michael plays Santa to Maria and Liz's elves at a charity event. Isabel and Jesse share their first holiday together as husband and wife.
In an attempt to find Roswell's legendary New Year's Rave, Max and Maria join forces. Meanwhile, Liz connects with her father and Isabel helps Kyle find the perfect date for New Year's.
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.
Michael, Jesse and Valenti call on a discredited doctor to help the wounded Isabel. Also, Clayton Wheeler undergoes an amazing transformation and soon finds himself drawn to Liz; and Jesse quizzes Michael about Isabel's alien roots.
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.