Liz has a summer job as the local Congresswoman's intern. She and Pearce have been working together, and she is suspicious when Nesedo-Pearce testifies to Congress that the Roswell evidence is a fake. Then the real Pearce's body is discovered in the desert, and Valenti is cornered into arresting Michael for murder. But Max "ages" the bones, destroying the evidence of a recent murder. But all is not well. A "Skin" kills Nesedo. And the Congresswoman Wittaker is still suspicious....
Liz still gets telepathic "flashes" when Max touches her, but pretends she doesn't. Max is suspicious of the new curator of the UFO museum. Is he an enemy? In parallel with school lessons on the Cuban missile crisis, Max wonders what to do to be a leader. The others try to convince Max that they must kill the curator. In the end, he doesn't, and discovers the curator believes himself to be an alien abductee. But we discover the new waitress at the Crashdown is a Skin. Liz tells the Congresswoman Wittaker that Pearce left her a voice-mail saying good-bye -- but Wittaker is still suspicious, and now of Liz....
Max throws Isabelle a surprise birthday party in the Crashdown. But she keeps having visions of Tess. She and Maria go looking for her, and discover that Wittaker is trying to learn the location of the Granolith from her. Wittaker tells Isabelle that in her previous life she betrayed her planet. Isabelle rescues Tess, and destroys the Skin Wittaker in a hail of dandruff. Then she discovers the Granolith back in the pod cave.
Michael interviews a WWII veteran for a school project, but instead learns more about the events of the saucer crash. In particular, there were eight babies, not just four. Also, Michael comes to realise how much he owes humans for his existence.
A future Max comes back to tell Liz that her relationship with current-Max will persuade Tess to leave, that her loss fatally weakens the team, and that the whole world is taken over by the enemy aliens. Liz must break up with current-Max, and persuade him to go with Tess. A broken-hearted Liz agrees, but has a hard time persuading Max of her decision. She finally has to pretend to go to bed with Kyle to convince him. Meanwhile, Michael investigates the new waitress and discovers she is a Skin, but not before Maria discovers them together.
The gang visit Congresswoman Whitaker's home town, to find out why her death is being covered up, and discover the whole town is full of Skins, who have nearly completed growing replacement "husks" for their own worn out ones. The waitress Skin is from a different group, supporting Michael over Max. The gang only just escape, but destroy all the husks except the waitress's.
Roswell suddenly becomes a ghost town -- only the four aliens plus humans who have recently returned are around -- and those humans start slowly disappearing, too. It's a plot by the husks to isolate them and kill them. The waitress tells them how to kill Skins, and is then captured by the Skins. She suicides rather than tell them the location of the granolith. Isabel pretends to defect, tries to kill the Skin leader, but is stopped. Liz, Kyle and Maria rush to destroy the Skins' power source -- killing all the Skins, saving the four aliens, and restoring the humans.
The other four pod people are a New York punk version of the Roswell four. They've been summoned to an interstellar peace summit, but NY-Michael killed NY-Max. So they come to Roswell to get Max to go in his place. NY-Isabel pretends to be Isabel, and makes Max distrust her. Max and Tess go off with the clones, but NY-Tess, frightened of the others, stays in Roswell.
Max goes to the peace conference, but refuses to give up the granolith. Liz tells Maria what really happened with Kyle, and why. NY-Tess tells the gang how NY-Max really died. Isabel tries to contact Max to warn him, but fails. Liz manages to get through, saving him from a falling balcony. Max asks to renew their friendship. Liz agrees, but still maintains her lie about Kyle.
[It's the saccharine Christmas episode.] Max sees a man die, and does nothing to save him, because he's frightened of being put back in the white room. But he's then haunted by the dead man, and makes up for his cowardice by curing some cancer patients. Michael has difficulty getting the right present for Maria, but Isabel helps him out. Tess brings a good old-fashioned Christmas to the Valentis.
A detective comes to question Sheriff Valenti, ostensibly about the Hubble shooting, but really about his relationship with Max. Meanwhile, Isabel has a vivid dream about a kidnapped girl. She tells Valenti, who manages to upset everyone in his investigation, yet turns up nothing. Maria's bad cousin Shaun shows up, and Liz is drawn to him. Then Isabel dreams again, and finally they find the real victim, Laurie DuPree, just in time. Isabel feels something strange about her. (There's a suggestion the kidnapper may be the geologist Grant.)
Valenti is in trouble about his investigations, but a hot-shot FBI agent gives him a second chance. Then Laurie DuPree vanishes from hospital, and comes to his house claiming to have been chased by aliens. She freaks when she sees Michael, and runs off again. A newly-cool Alex returns from a month in Sweden. Valenti is sacked as Sheriff. Michael breaks in to the psychiatric hospital where Laurie has been takes, and finds a picture of Laurie's grandfather -- that looks exactly like him.
Michael and Maria flee with Laurie DuPree, and take her to her grandfather's house. But he is long dead, and her uncle and aunt are not best pleased to see her, or Michael, who they assume to be an illegitimate family member on the make. Valenti manages to convince the FBI agent to investigate the geologist. Isabel and Max learn the crystals, infecting the water table, are a great danger to them.
Alex and Kyle get trapped in a cave of the blue crystal creatures, and learn that lack of oxygen kills them. Michael and Maria get back to see Laurie, and learn that her "bad blood" genetic defect is what makes her attractive to the crystals. Isobel is kidnapped by the geologist, on his way to infect Laurie, but manages to warn Valenti. He and the FBI agent arrive in time to save Laurie.
Michael is suffering nightmares from getting shot, so he persuades Max to skip classes and go with him to Las Vegas for a holiday, to blow the $50,000 Laurie's relatives gave to buy him off. One by one the rest of the gang hear about it, and all decide to go. Various adventures and reconciliations ensue, until Sheriff Valenti turns up.
It's time for The Prom. The expected couples go together, but learn new things. Maria is upset that Michael is absent, but then he turns up, explaining he needed dancing lessons. Alex is dubious about taking Isobel, in case he becomes a lovesick fool again, but does so anyway. Kyle learns he thinks of Tess as his sister. Liz and Max finally finally break up, with Max remembering his first kiss with Tess back on their home planet, and Liz going off with Shaun.
Alex is killed in a car crash. All the evidence points to suicide. Liz is convinced it's murder, however. She wonders if it might have something to do with aliens -- Max is horrified by the idea.
Liz continues to investigate Alex's death, her obsessive behaviour destroying her relationships with everyone else. She finds a link to his Swedish exchange, then finds evidence he might never have gone to Sweden at all.
Liz and Maria track Alex's past movements to the local university, where he was using the supercomputer to decode the alien book. Kyle persuades Isabel to use her powers to play pranks on Max. Max and Tess get close, and Tess gets pregnant, but the fast-growing alien foetus is being poisoned by Earth's atmosphere. Michael gives the decoded book to Max, who realises it tells them how to get home.
While trying to recreate details of his abduction, Brody is affected by a freak accident, and gains memories of his alien abductor. Confused and hostile, he holds some of the gang hostage in the UFO centre. Alien abilities come in useful.
The aliens have the one chance to use the granolith to go back home, and Max says it has to be now, to save Tess's baby. They start saying goodbyes. Then Kyle has flashbacks of Alex, and the humans discover it was Tess who killed Alex, while mindwarping him to translate the book. Max confronts Tess, who admits that Nesedo made a deal with their enemies. He sends her back alone, stranding the original three...