S7E1 · The Sixth Extinction

On the coast of Côte d'Ivoire, Scully sits in her tent studying detailed photographs of the spacecraft half-buried in the beach nearby. A figure, the Primitive African Man, mysteriously appears before suddenly vanishing, after which Scully's tent is swarmed by flying insects. Back in the U.S., Walter Skinner visits a delusional Fox Mulder, who is being kept in a padded cell at a Georgetown hospital. Mulder seemingly attacks Skinner, but actually covertly passes him a torn shred of his hospital gown reading, "HELP ME".

Scully is visited by Dr. Amina Ngebe, Solomon Merkmellen's former colleague, who warns her to not tell any of the locals about the swarm or the Primitive African Man, although word is already out on the "African internet". Soon afterwards, one of the locals working on excavating the ship is apparently scalded by boiling seawater. With the arrival of Dr. Barnes another "plague" occurs: that night the ocean turns blood red.

Skinner revisits a heavily drugged Mulder, who cannot talk but writes "Kritschgau". Skinner visits Michael Kritschgau, now unemployed and living in a low-cost apartment, and convinces him to visit the hospital with him. Once there, Kritschgau believes Mulder has alien-induced mind reading abilities and injects him with phenytoin to slow down his brain activity. Later, Diana Fowley and his doctor arrive, and with his mind-reading abilities, Mulder tells Skinner that he knows about him being indebted to Alex Krycek, and Fowley's connections with the Smoking Man.

Scully, with Barnes' help, is able to translate some of the inscriptions on the spacecraft, which contains information on genetics and various religions. However, Barnes' behavior becomes increasingly erratic and, arming himself with a machete, he refuses to let Scully or Ngebe leave. Barnes realizes that the craft is bringing dead fish back to life. Scully and Ngebe take the opportunity to knock him out and escape. Scully sees the Primitive African Man again in the car as they drive off.

Skinner and Kritschgau put Mulder under additional tests to verify his abnormal brain activity. They again inject Mulder with phenytoin, but this time they are caught by Fowley; Mulder goes into a seizure. Meanwhile, Barnes, in a bizarre experiment, kills his driver, only for the driver to soon reanimate and kill Barnes instead. Scully flies back to the U.S. and visits Mulder at the hospital. On the African coast, Ngebe arrives with the police, finding Barnes dead and the spaceship gone.