Father Joe: So you believe in these sort of things?
Mulder: Let's just say I want to believe.
It features series protagonists Fox Mulder and Dana Scully long after they abandoned the FBI and the X-Files; Scully is a doctor at a Catholic hospital concerned about the treatment options offered to a dying boy, and Mulder, still on the lam, lives as a hermit under Scully's protection, doing little more than collecting paper clippings. They are offered a chance at redemption, however, when the FBI requests their help in finding an old comrade, who has herself gone missing while investigating a series of mysterious disappearances. They are aided by an ex-priest and convicted pedophile named Father Joe (Billy Connolly), who claims to receive psychic visions of the victims directly from God, and about whom the agents have conflicting feelings.
The X-Files: I Want to Believe contains examples of:
- Aborted Arc: Scully and Mulder both appear to be completely unconcerned about the supposedly inevitable extraterrestrial colonization of Earth coming in four years. It's not even mentioned.
- Beard of Sorrow: Mulder has grown one, over his continued search for the truth that has not gone anywhere since 2002.
- Black Speech: The deadly medical staff speak Russian and Czech in a post-Cold War East-West paranoia way.
- Blatant Lies:Skinner: It's Mulder. He wouldn't do anything crazy.
- The Cameo: Vanessa Morley, who played Samantha Mulder as a child, is seen briefly walking past Mulder and Scully in the FBI office.
- Continuity Nod: Several little ones.
- In Mulder's room, there are multiple pencils stuck on the ceiling.
- Whitney namedrops other psychics Mulder has dealt with before: Luther "Lee" Boggs, Clyde Bruckman and Gerald Schnauz.
- There is a brief conversation between Mulder and Scully about her son William, and how Scully gave him up to another family for his protection.
- Creative Closing Credits: The credits play over snowy and watery environments, like waves crashing on rocks. In the extended cut, a slideshow of photos of the film's production appear around the credits.
- Darker and Edgier: Than most of the TV series - in tone as well as lighting. The villain's plan is grotesquely twisted than other villains Mulder and Scully have seen before: grafting female body parts with his own, all to live longer.
- Deadly Doctor: Deadly doctors and nurses, who want to prolong Franz Tomczeszyn's life by kidnapping women and transplanting their organs and body parts onto him.
- Death Equals Redemption: Father Joe wants to do some good before he dies.
- Distressed Dude: Scully had the Distress Ball in the first movie, so it's Mulder's turn now, after he attempts to break in Janke Dacyshyn's compound.
- Gondor Calls for Aid: Skinner makes a surprise appearance in this role, after Mulder is caught by the enemy.
- Hidden in Plain Sight: Mulder's in hiding from a death sentence. Surely no-one will ever think to look for him at Scully's house! Handwaved by the suggestion that the FBI is just glad to have him out of their hair, although given why he's under a death sentence that doesn't really explain much.
- Last-Name Basis: Despite the obvious Relationship Upgrade, you won't hear Mulder or Scully call each other "Dana" or "Fox" even once.
- Meaningful Name: The Littlest Cancer Patient causing a schism in Scully's faith in God and her faith in science is named Christian? Really?
- Mortality Phobia: The plot of this movie concerns a Russian who doesn't want to die, so he has his medial mooks kill people and graft his head onto their bodies so he can live a little bit longer. They've done this several times before the start of the film and a couple more times during the film before they're stopped in the end. It appears they're just doing it For Science!, they don't especially care about the guy or payment.
- Never Trust a Trailer:
- Despite rumors and the domestic trailer portraying the movie (correctly) as an upgraded Monster of the Week, the international trailer went out of its way to make it look like a movie about aliens.
- One trailer implied that Mulder and Scully had gone their separate ways after the end of the series and were reuniting, much to the outrage of fans. Luckily, that's disproven within the first few minutes of the movie.
- Refusal of the Call: Scully wants to focus more on her neurosurgeon job than solving Father Joe's case.Scully: This isn't my life anymore, Mulder. I'm done chasing monsters in the dark. I think you've done all they've asked of you here too. You know, no-one says you have to stay here.
- Relationship Reveal: Mulder and Scully. (It was strongly implied that they'd gotten together in the last few years of the show, but it took until this movie for the writers to finally stop trying to be coy about it.)
- Pedophile Priest: Father Joe. As Scully puts it, "[she] didn't bugger thirty-seven altar boys".
- Second-Act Breakup: It does seem to be fixed by the end, though.
- Shout-Out: See the sub-page listing Shout Outs from the whole franchise.
- The Stinger: Not plot-related, anyway. It only shows Mulder and Scully on a boat, referencing one of Mulder's last lines in the movie about the two of them "get[ting] out of here" should Scully have doubts about Christian's surgery. As the camera pans further into the sky, Mulder and Scully look up and wave to the audience.
- Surgeons Can Do Autopsies If They Want: Scully, a forensic pathologist during the show, is now working in the field of pediatric neurosurgery. Although enough time has passed that she might have returned to school or something, it's not explained or even alluded to.
- Tears of Blood: Happens to Father Joe during his psychic visions.
- Violently Protective Girlfriend: Scully knocks a man unconscious with a piece of firewood to stop him from killing Mulder.
- What Happened to the Mouse?: No information is given on the whereabouts of Doggett and Reyes.