With Scully back in the X-Files, Mulder and her flies to the site of an erupting volcano in Oregon to investigate the mysterious disappearances of several scientist who were studying the volcano. Mulder and Scully discover a deadly life form that can survive in the searing heat of the crater and is killing the scientists to avoid being discovered.

As the Dark Phoenix grows increasingly hostile, even destroying an entire star system, the X-Men struggle to figure out a way to stop her without harming their teammate Jean Grey.

Josh is back on the ambulances and has a new partner Liz Harker as Matt is found to having some trouble at home with his parents.