Max tries to protect Michael, Isabel, Tess and himself by covering up the murder of Agent Pierce only to have Nasedo reveal that there is yet another enemy tracking down the Royal Four.

After Nasedo's death Max senses he has to assume more of a leadership position and also realizes that Tess will be safer if she moves in with Sheriff Valenti and Kyle.

A surprise birthday party for Isabel brings everyone together at the Crashdown, but she had already made plans that stun Max and their mom. Liz discovers that Congresswoman Whitaker has been recording her phone conversations. Michael confronts Courtney after finding pictures of her in Whitaker's office. Isabel has visions of Tess pleading for help. Against Max's orders, she goes in search of Tess and is confronted by one of the Skins.

Michael is assigned to talk to a WWII vet for history class and hears the story of the crash of the alien craft in 1947. Michael imagines the story with himself and his friends in the roles. The military actions and cover up surrounding the crash is revealed and Michael learns more than he bargained for about his own history and what else might be out there.

Max visits Liz from the future to persuade her to break up with him, which could result in the world being saved.

The teenage aliens travel to the Skins' organization and destroy the husk factory. Skins' leader Nicolas determines to pursue them.

The teenage aliens flee back to Roswell, where they find all the humans gone. They surmise that their disappearance is due to the Skins, who want to isolate the Roswell aliens, making them easier to find. Nicolas leads the Skins in the hunt but is unable to see the royal aliens due to a mind push. Courtney protects the Granolith.

The punk, duplicate aliens from the second set of pods come to Roswell to persuade Max to come away to an interplanetary peace summit in New York.

Max and Tess arrive in N.Y.C. to meet with the leaders of their home star system, unaware that Max's counterpart was killed by the other three counterparts and Max is in similar danger.

The Roswell aliens celebrate Christmas with their friends and families.

Isabel enlists Sheriff Valenti's help after she receives numerous flashes of a young girl being kidnapped then buried alive somewhere near Roswell.

Laurie Dupree, the girl who Isabel and Sheriff Valenti saved, suddenly claims she is being pursued by aliens and the conflicting information on the case causes Valenti his job.

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 investigating Alex's death Liz uncovers information that leads her to believe that the semester Alex supposedly spent in Sweden never really happened.

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.