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).