A young FBI agent is assigned watchdog duty over a fellow agent, but finds herself drawn into his investigations of paranormal and unexplained phenomena.
While negotiating a tense hostage situation, Mulder finds himself sympathizing with a gunman who claims to be the victim of alien experimentation.
The agents face their old foe, Alex Krycek, while pursuing a radioactive entity unleashed from a sunken WWII wreckage.
When Lt. Colonel John Sheppard (Joe Flanigan) is informed that his father has passed away he packs a few things and accompanied by Ronan (Jason Momoa) heads back to Earth to attend the funeral. There Ronan gains some insights to his friend's past - Sheppard's troubled relationship with his father and brother as well as his ex-wife Nancy a director with Homeland Security. Before long they are approached by a woman Ava Dixon who claims to know about a covert project involving nanite programming. Sheppard's worst fears are realized when she leads them to a high tech lab and reveals that she and her partner have been successful in creating a human form Replicator - a Replicator now loose somewhere in the city who must be recaptured at all cost.
After visiting an old flame who's now working as a Park Ranger, MacGyver finds himself in the middle of a grizzly poaching investigation.