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 takes a job as a security guard at a pharmaceutical company, Isabel and Jesse’s relationship deepens, and Liz and Max secretly meet each other despite Liz’s father’s objections.

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.

Kivar, in human form, voluptuously inhabits Isabel's dreams and attends the wedding.

Kivar shows up in the form of Denny, a missing Roswellian, and causes galactic problems for the honeymooners.

Guitar-playing Billy, an old friend and flame of Maria's, shows up and causes havoc between her and Michael.

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.

Everyone ends up spending New Year’s Eve with someone else’s significant other: Maria and Max go to a rave, Isabel watches a movie with Kyle, and Liz watches over a passed out Michael.

Eric, an old frat friend of Jesse's and an investigative reporter, comes to Roswell, needing a big story to save his job, eventually settling on Isabel, Max, and Michael as "the Roswell Aliens".

When Liz begins to feel ill she suspects it is connected to when Max brought her back from the dead, and Maria gets an opportunity to pursue her life’s big dream as a singer.

Two thousand miles away from Roswell Liz settles in at Winnaman Academy while Maria has a disappointing experience in New York City at her first professional recording session.

As the group tries to save Isabel's life after she is shot, Jesse discovers the truth, and Max's mind begins to resurface in the evil Clayton Wheeler's body.

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.

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).