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.
While Max, Michael, and Maria go in search of a secret New Year's Eve party in the desert, Liz is stuck at the Crash Down with her dad facilitating a party for residents of a retirement home. With Jesse stranded at an airport in Houston, Isabel decides to help Kyle find a girlfriend. Liz's dad talks to Valenti about Max.
Liz seems to be going through some... Changes. Developing alien powers wasn't something she expected, but it's definitely happening. Michael thinks that Liz might be dying and Max is determined to save her. Kyle worries that this will eventually happen to him as Max saved his life as well. Meanwhile Maria gets a chance at a record deal and is completely oblivious to what her best friend is going through.
Maria is off to NYC to pursue her music career, but begins to question what they are asking her to do. Liz heads to a boarding school in New England to get away from Max and seems to be healed from whatever was ailing her back in Roswell. One of the other security guards is killed at the biomedical plant where Michael works and he enlists Valenti to help him find out what happened, but discovers they have been studying him and may know he's an alien.
Michael realizes that he became the leader when Max died and begins to take matters into his own hands, rebelling against the resurrected Max. Jesse is having a hard time dealing with the news that his wife is an alien. Michael fears Jesse is telling his therapist too much so he threatens the therapist, who alerts the FBI causing big problems for the whole group.
Michael witnesses an Air Force plane crash into a UFO in the desert. The Air Force reports that the pilot died, but Michael searches for him, helping the pilot's daughter to learn the truth. While Jesse is out of town with her father, Isabel spends time with her mother. Both are interrogated about their lives by her parents.
The scientists studying the crashed UFO discover a baby inside, but to protect the baby, the other passenger kills them all and takes the baby on the run. Just as their parents are confronting them with a video of Isabel using her alien powers, Max hears an intruder and goes to the kitchen to find Tess holding the baby. There is little time to explain to their parents as they need to get out before the Air Force comes into the house searching for the alien. So now the group of friends must decide what to do with Tess as several of them want her to pay for Alex's death...
Liz has a premonition where she, Max, Michael and Isabel are all viciously murdered. Thinking that this event will take place in two weeks the group decide they must leave Roswell one by one right after graduation to save themselves and everyone they love. They find out only too late that their deaths, in actual fact, occur during graduation (which they are all attending at the time of realization).