A law officer arrives in Roswell and questions Sheriff Valenti about a death -- which the sheriff had covered up for Max a year earlier. Simultaneously, Isabel reports to the sheriff a girl that has been buried alive -- but whom Isabel has only seen in her dreams. Valenti's job is jeopardized when he pursues Isabel's lead.
Sheriff Valenti is suspended from his job after the incident with the girl who was buried alive. Isabel can't stop thinking about her and when she disappears from the hospital, the FBI gets involved in the search and Valenti is temporarily reinstated to help. When the teens keep showing up, suspicions mount concerning his relationship with the youth and his job is threatened. Alex returns from a trip to Sweden and his experience makes Liz think about traveling the world while Sean continues to pursue Liz.
Laurie breaks away from custody and reluctantly goes with Maria and Michael. They end up at her grandfather's house in Tucson where her aunt and uncle show her very little love. Meanwhile, Max enlists Liz's help to investigate the blue crystal that Michael found at Laurie's burial site. Valenti grows even more suspicious of Sorenson when he attacks Valenti in a momentary fit of rage. Valenti convinces FBI Agent Duff to investigate Sorenson further and she discovers an interesting pattern in his travel.
Maria and Michael investigate Laurie's situation and find that the house really belongs to her, but her aunt and uncle paid to have her declared insane. Michael discovers the manner in which he is related to Laurie. Brody's body is possessed again and Max, Isabel, Tess, and Liz learn about the parasitic nature of the blue crystals and why they infected Laurie, but not all human beings. They enlist Alex and Kyle to help them search for the hive so they can stop the deadly spread of the parasite.
Michael feels like the $50,000 payoff from Laurie's aunt and uncle is haunting him and decides a trip to Las Vegas is in order. The whole gang ends up going, but Michael's special guy's vacation hits the rocks when he and Max argue after being arrested in the casino. The trip brings back memories for Liz of when future Max revealed they had eloped in Vegas at age 19.
The prom is approaching fast and our Roswellian friends are extremely excited, each looking forward to it for different reasons. Liz is going to ask Max to go with her, but her night ends very differently to the way she hoped it would. Maria wants Michael to go with her, but suspects he's having an affair. Kyle finally decides to tell Tess how he feels about her, only to discover that he was confused about his own feelings. Isabel finally 'sees' Alex.
When one of their closest friends die in suspicious circumstances, each character deals with it differently. Liz is in denial, refusing to believe that her friend would commit suicide; Maria falls apart, leaning on a surprisingly caring Michael for support; Isabel believes her friend's death was her fault; Kyle tries to stay strong and Max finds himself jealous that Sean is there for Liz when he can't be. Liz makes an accusation that could ultimately crush her relationship with not only Max, but the entire pod squad.
While Liz is obsessed with investigating Alex's accident, but when she enlists Sean's help to break into the school for evidence, they are caught which causes problems for Sean. Liz finds that something isn't right about Alex's trip to Sweden. Isabel continues to talk about going to college in San Francisco, but both Max and Michael tell her she can't go. Maria has trouble dealing with the loss, Liz's obsession, and Michael's sudden caring nature. Max continues to deny it could be alien involvement that caused Alex's accident.
Liz continues to pursue her theory that Alex's accident was caused by an alien. Maria joins her investigation when they discover that Alex was at the University of New Mexico in Las Cruces instead of in Sweden. So Liz and Maria head to the University to find out what Alex was doing there and Michael follows them. After an intimate night together, Tess tells Max she's pregnant and forces him to consider their future.
In events that are supposed to have taken place before the last several episodes (pre-prom), Brody remembers being controlled by the alien Larek and holds Max, Tess, Maria, Sean, and Maria's mom hostage at the UFO center. He demands to be told why he has been abducted and lied to.
Max, Michael, Isabel, and Tess prepare to return to their home planet using the granolith and the directions from the book that Alex translated. They find that saying goodbye is not an easy thing to do. Max and Liz discover that the university student they believed to be an alien is not and therefore couldn't have been Alex's killer. Kyle and Maria's mom start to remember things that Tess had mind warped them to forget.
Liz and Max get caught while apparently robbing a quick stop that happens to have a government storage facility with a space ship underneath it. The past three months are reviewed in flashbacks explaining how and why they have gotten to this point. Max's charges are dropped, but Liz is held because she was allegedly holding a gun. Meanwhile, Isabel has a new haircut and a new boyfriend - a secret one who works for her father.
Michael decides to take a night security job at a medical company to make some extra money. He isn't fond of the boring uniform or hours, so he endeavors to lighten things up a bit, but manages to get himself and all his co-workers fired. He hatches a plan to get their jobs back, but it just may involve some illegal activities. Liz's father has forbidden her to see Max, but they covertly continue to meet. Kyle discovers Isabel's secret boyfriend when he happens upon them at a convenience store.
Isabel struggles as her relationship with Jesse becomes more serious. She continues to see and talk to Alex about what's going on in her life. Michael and Max insist she not tell Jesse about their origins. Liz's dad holds his stance on her not seeing Max, but she continues to rebel and they argue. Michael enjoys the company of his new co-workers at the expense of time with Maria.
Max heads to Los Angeles to try to locate the second shape-shifter to find out how to contact his son. Back in Roswell, Kyle and Liz discover information about a murder that the shape-shifter may have committed in 1959. Kyle's grandfather, sheriff at the time, believed it was an alien who killed the actress, but was ridiculed.
Max strikes out alone for Los Angeles in search of the second shape-shifter, inadvertently discovering that he, the shape-shifter, is programmed to be a slave over whom Max has absolute control. With his unwilling help, Max attempts to use the saucer to return to Antar to contact his son.
A young autistic boy approaches Max at the Crash Down and speaks to him. Max believes it may be his son trying to communicate through the boy. Jesse is not impressed by Isabel's hectic holiday schedule and tries to get her to relax. Michael takes on the role of Santa to be close to Maria, who is volunteering as an elf with Liz.