Liz Parker, the "smallest of small town girls", waitresses in her parents' "Crashdown Cafe" in Roswell, NM. One busy day in the cafe, a couple of yahoos start a fight and one of them fires a gun. The stray bullet hits Liz and she starts to bleed to death. Max Evans, a classmate at West Roswell High who's been keeping a close eye on the beautiful Liz, rushes to her aid. Putting his hand over the wound, he heals Liz but leaves a silver handprint on her skin. No one saw him do this with certainty, and he asks Liz to keep it a secret. But Liz has to know. Who or what is Max Evans?
     Confronting him at school, Max reveals a secret to Liz that he and two others have kept from everyone for 11 years. Max, his sister Isabel and their friend Michael Guerin are not from this earth. They believe they are aliens connected to the '47 crash, but only know they emerged from incubation pods as 6 year old human children and were found wandering alone in the desert. Max and Isabel were adopted by the Evans, but Michael was passed from foster home to foster home, ending up in trailer park hell with an alcoholic foster dad.
     Liz confides in her best friend Maria, but she has to be careful of Kyle, her jealous ex-boyfriend who suspects something different about Max Evans. This seems to be the least of their worries though, as Kyle's dad, Sheriff Valenti, driven by his own personal demons, puts the evidence surrounding the shooting together to paint a picture close to the truth. By alerting the FBI, he unwittingly launches an alien hunt carried out undercover by Special Agent Kathleen Topolsky posing as a guidance counselor at the high school.
     At a time when the three young aliens should be keeping things quiet, Michael is obsessed with uncovering clues to their origins because, "there has to be something more out there than Roswell." When he finds a key hidden in the Sheriff's office, he has a vision of a geodesic dome in Texas where he is positive secrets are hidden. After finding the dome, they discover items there that could answer their questions, including a pendant with a familiar symbol on it. Mysteriously, the box of materials they collected at the dome is stolen in a fake break-in of Max and Isabel's house, leading to the certainty that the Feds are after them.
     Despite this theft, evidence is mounting that leads them to believe there is a fourth alien, one called "Nasedo" by River Dog, an Indian from the local reservation. Michael is driven to find Nasedo, but the stories point to Nasedo being a dangerous shapeshifter and possibly a murderer. Max tries to convince Michael to take it slow, but it's nearly impossible to do so.
     Enlisting the help of Alex Whitman, a friend they've left in the dark about the Aliens' secret, Liz is able to blow Agent Topolsky's cover at the high school. Eventually Liz reveals to Alex the secret about Max, Isabel and Michael. By this time, the attraction between Max and Liz is undeniable, while a much rockier relationship between Michael and Maria also heats up. Naturally, Isabel and Alex turn to each other for comfort and support.
     But Topolsky returns to Roswell after having been tortured by the head of the FBI's alien hunting special unit, Agent Pierce. In a crazed state, she warns Liz and the others that they are in grave danger from Pierce. She convinces Michael that she has an alien "communicator", an object exactly like one that Max and Liz found. This prompts Michael to break the covenant of secrecy and meet with Topolsky so he can find out how the communicators work. The Sheriff interrupts his plan and takes possession of Michael's communicator. Later, after Kathleen Topolsky disappears and Sheriff Valenti finds out that she has been killed, the Sheriff realizes he's been wrong to support the alien hunters seeking Max. He tries to convince the gang to trust him and returns the communicator to them.
     Just when Max and Liz feel the most committed to each other, a new girl, Tess, arrives in town and has a strange power over Max. He can't help being attracted to her and Liz catches Max kissing the new girl. Tess endears herself to Isabel and admits she is drawn to Max. In the meantime, Michael and Isabel have dreams about being with each other, leaving Maria to feel left out of Michael's affections. The gang discovers that Tess is an alien and, like them, she has unusual powers. They realize the man posing as her single dad is really Nasedo, the shapeshifter.
     Tess has good reason to pursue Max. She has access to an alien book that reveals that she, Max, Isabel, and Michael were engineered for a purpose, and that she was meant to be partnered with Max, as Michael was destined to be with Isabel. Liz struggles with the concept that Max may have a destiny apart from her, but Max assures her that he only wants to be with her.
     Pierce catches up with his target, Max, and takes him to a deserted military facility where he uses torture to extract information from him about his alien identity. While Max is in a drugged state, Isabel uses her powers to enter his mind and find out where he is. With the help of Nasedo and Sheriff Valenti, the gang, including Tess, rescues Max. But Agent Pierce keeps hunting them until Michael, who can't control his tremendous power, kills Pierce in anger.
     Tess leads Max, Isabel, Michael and Liz back to the cave in the desert where the empty incubation pods have been hidden, undisturbed. Here, they realize that Tess was with them from the beginning. Here they also learn that Nasedo was the only survivin alien of the 1947 UFO crash near Roswell. Nasedo shapeshifts into the form of Agent Pierce and leaves to take Pierce's identity in the FBI where he will pull back the hunt for Max and the others.
     Having both communicators in their possession at this moment, they use them to receive a message from their home planet sent by Max and Isabel's alien mother. She tells them they were the leaders of their people: Max, the head, Tess, his wife, Isabel, his sister, and Michael, Max's second in command. They were killed on their home planet, but their "essence" was infused with human DNA on earth in hopes that they could return and become leaders again.
     Feeling eclipsed by the destiny she thinks Max will have to follow with Tess, Liz leaves the four others behind, returning to Roswell with a broken heart.