The X-Files miniseries' finale episode featured a worldwide epidemic and a planned move by the Cigarette-Smoking Man, before ending with a mysterious UFO appearing in the middle of a highway with a spotlight pointed directly at agent Dana Scully.

In episode 6 titled My Struggle II, when people start falling sick with a variety of illnesses, Scully theorises that someone high in power was trying to kill everyone using a Spartan virus. After a visit from her old friend Monica Reyes, Scully realises that her unique gene was shielding her from falling sick. She alongside agent Einstein then synthesises a vaccine from her DNA and starts healing everyone.

On the other hand, Fox Mulder goes after the Cigarette-Smoking Man with guns blazing and denies his offer of joining his team. Meanwhile, Mulder gets infected by the virus and ends up in a very bad shape before Scully brings him the antidote.

Scully then informs agent Miller that Mulder's condition was worse than she had anticipated and that the only way for him to survive was an infusion of their son William's stem cells. In the midst of all this, a UFO spaceship appears out of nowhere.

In an interview, creator Chris Carter talked about the ending and hinted at more X-Files episode in the future. Carter told TV Line: "Fox owns this show. I can't imagine, with the ratings that we've got and the way we ended this season, that there won't be more X-Files. They will find a way to get that done. Because I spoke about it briefly with [Fox CEO] Dana Walden today, so there's an appetite there and... a chance certainly to find how we're gonna get ourselves off this precipice."

When asked about William's whereabouts, which was a constant reference throughout the season, Carter just teased: "I can't tell you," and added: "Well, if anyone knows [about William] it's me." Given Mulder's condition and talks about more episodes, William will have to make an appearance to save his father's life.

The creator also spoke as to why only Scully was immune to the Spartan virus and not Mulder. Leaving the door for season 2 open, Carter said: "That's a good question. And one that needs to be answered." Fans will remember that even Mulder was abducted by aliens at some point in The X-files 9 season run.