After spending the summer at her aunt's in Florida, Liz returns to Roswell, New Mexico. When Max catches her on the street shortly before her interview with Congresswoman Whitaker, he informs her nothing 'alien' has happened during her absence. Max then asks Liz to give their relationship another chance, but she reminds him of his destiny. Liz stands by her decision the two of them cannot be together, even later when his touch gives her flashes of the good times they shared over the past year. Meanwhile, a handsome geologist uncovers a human bone in the desert with a metal detector. The confused geologist is lead to Valenti by a somewhat smitten Isabel who has just told Alex she is not interested in dating. Valenti immediately connects the bone to the skeleton of Agent Pierce who he, Max and Michael burned and buried earlier that year. Before Valenti can cover up the finding, Deputy Hanson insists the bone be tested and the area excavated.
When Michael voices his concern over the bone and the geologist, Max demands they wait to see what will unfold. Tired of Max's insistence they do nothing, Michael goes to the excavation. While there he discovers a skin-like material on the ground, which dissolves at his touch. Later when Michael's pocketknife is recovered at the scene, he is arrested and thrown into jail for murder. Meanwhile, still posing as Agent Pierce, Nasedo dissolves the Special Unit of the FBI. After receiving an urgent call from Michael, Nasedo returns to Roswell. The kids then learn that Congresswoman Whitaker and Agent Pierce were having a relationship, as Whitaker becomes determined to prove the bones contain a chemical not found on Earth called Cadmium X. Learning of Whitaker's plan, Max goes to Liz for help in locating where Whitaker has taken the bones.
After learning the location, and with the help of Isabel and Tess, Max breaks in and alters the bones carbon dating so they appear to be over 40 years old; old enough to have been effected by nuclear testing that occurred in New Mexico during the war. Now unable to confirm her theory, Whitaker sets Michael free. Michael joins the others, minus Max, at the Crashdown where we meet a new waitress Courtney. Maria then asks Michael if they can possibly renew their relationship, to which he replies no. In the end, thinking Michael has come to pay him a visit, Max opens his bedroom window to find an injured Nasedo. Nasedo informs Max "they" are among them now, meaning the Skins. Nasedo then dies in Max's arms.
- This is the only season premiere not to feature Jeff Parker