Parece que Mulder estava sofrendo de "aumento da atividade cerebral" e um início de telepatia causado pelo óleo negro "reavivado" que ele infectou no episódio "Tunguska" três anos antes.
Aqui está o detalhamento:
Mulder is being held in a padded cell and is displaying abnormal brain activity.
Kritschgau believes Mulder has alien induced mind reading abilities and injects him with a drug (phenytoin) to slow down his brain activity.
A Sexta Extinção II: Amor Fati
Scully returns from Africa to discover Mulder in a coma induced by exposure to shards from an alien spaceship wreck
E
Kritschgau visits Scully and claims that Mulder's contact with the shard of an alien spaceship has reawakened the extraterrestrial black oil with which he was infected three years previously; because he is infected with the virus, Mulder is proof of alien life
E
Mulder is revealed to be dreaming everything: in reality he is in a government facility being tended to by doctors while The Smoking Man and Fowley watch. The Smoking Man is preparing to have portions of Mulder's cranial tissue—which have been infected and activated because of the alien virus—implanted into himself. During the operation, The Smoking Man admits that he believes that Mulder has become an alien-human hybrid, and that by taking Mulder's genetic material he alone will survive the coming alien onslaught.
Portanto, uma resposta curta, o contato com os fragmentos da espaçonave africana, reavivou a infecção pelo óleo negro que até agora estava inativa.