In the concluding part to last season's cliffhanger, Mulder and Scully must protect Jeremiah Smith who is capable of healing Mulder's dying mother and to prove the existence of alien life.

With Mulder and Smith leaving on a boat, Scully is left with the alien bounty hunter. Apparently dead she checks on him when he suddenly opens his eyes and puts his hand round Scully's throat determined to find out where Mulder is heading off to as his orders are to kill off Jermiah. She won't tell him.

Meanwhile, Mulder and Smith head off to an eerie remote farm yard field where Smith promises Mulder that he will see his sister there. Discovering the remains of the electrician who was killed by a killer bee, they soon stumble upon the isolated community where they find a large area of crops being grown for pollen and Mulder's sister, Samantha working for them. Thinking she is his real sister, Mulder runs up to her but he is disappointed when he finds out that she is a clone of Samantha, a 'worker'.

Scully leads her own investigation into Jeremiah Smith and finds that he alone was secretly cataloguing the population using information taken from small-pox vaccination scars, including Scully's. Scully presents this new information to Skinner and some other officials of the FBI but they are in disbelief that we are all being actually catalogued.

Mulder and Smith are chased by the bounty hunter before they can find out more about Samantha where they hide in a bee apiary. Following them in, the bounty hunter gets trapped and is stung repeatedly by the bees as Mulder, Smith and the Samantha clone they took with them watch.

Meanwhile, the Cancer Man and one of the Elders have found out that X was the one who was leaking information to Mulder all along so when X calls on Mulder who is not there, he is gunned down by the Gray-Haired Man and killed leaving him lying in a pool of blood. Just before he dies he writes the letters 'SRSG' on the floor.

Mulder, his mother still in a coma, goes to visit the Special Representative of the Secretary General where he meets with a woman who identifies herself as Marita Covarrubias. She denies that the farmland in Canada ever existed just before she hands Mulder a folder containing photos of the Samantha clones and the farmland. She remarks that "Not everything dies, Mr.Mulder".

Finally, we see the bounty hunter enter the room to where Mulder's mother is lying. The Cancer Man is there where he tells him that "the fiercest enemy is the man who has nothing left to lose". The bounty hunter heals her and she awakens. The truth remains buried....