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Tear Jerker: The X-Files
"Conduit" offers us a pretty melancholy ending, with Mulder sitting in an empty church at night, gazing at a picture of him and his sister as children. He then breaks down crying, thinking about how much he wants to find her. As this is happening, we hear a tape recorder playing one of his sessions with a hypnotic therapist. It's the score that really helps accentuate Mulder's loss.
Therapist: Can you see your sister?
Mulder: No. But I can hear her.
Therapist: What is she saying?
Mulder: She's calling out my name... over and over again. She's crying out for help, but I can't help her. I can't move.
Therapist: Are you scared?
Mulder: I know I should be, but I'm not.
Therapist: Do you know why?
Mulder: Because of the voice.
Therapist: The voice?
Mulder:The voice in my head.
Therapist: What's it telling you?
Mulder: Not to be afraid. It's telling me that no harm will come to her, and that one day she'll return.
Made all the more effective with Mark Snow's score, with the sounds of the flute and synthesizer gently building as we hear more of Mulder's recorded interview with a therapist. As it starts to fade off, Mulder drops the "I want to believe line" for the first time in the series.
The episode "Roland" was heartrending, especially the end where Roland leaves his home and gives Tracy his jar with the stars. Horrible that they like each other so much and must be separated.
If you've lost a parent, Scully's storyline in 'Beyond the Sea' is heartbreaking. Especially her ending lines, "He was my father."
Whenever Scully breaks up and is Not So Stoic, chances are it's going to be a Tear Jerker. Just look at the ending of "Irresistible". She is always such a strong and capable woman, and very hard on herself. When she finally let Mulder comfort her...
Mulder while Scully is abducted. He just loses it. In "3", he's offered a hotel room while investigating a case out of state. His response? "I don't sleep anymore."
"Clyde Bruckman's Final Repose": Mr Bruckman's ultimate fate. After life seeing deaths, at times extremely gruesome, he felt Driven to Suicide.
"Wetwired": Mulder's distress when he's about to identify body that could be Scully. Even though it's something of an Audience Reaction of Like You Would Really Do It, his emotions are genuine.
The end of "Paper Clip."
"Memento Mori" is the episode where Scully's cancer is diagnosed. It is a direct and shameless heartstring-twister from start to finish. It works.
All of "Kaddish", especially the story behind the wedding ring. Poor couple, they could have been so happy together.
The scene in "Redux II" where Scully tries to get Mulder to pin the death of a man he killed on her — because she doesn't want him to go to prison, and she's going to die soon anyway. The look on Mulder's face is just heartbreaking.
In "Redux II", Mulder sobbing at Scully's bedside while she sleeps.
The ending of the episode "The Post-Modern Prometheus". The whole scene works on two levels and depends on how one interprets the writing. It feels very heart-warming, but considering that it's what Mulder told the writers (the boy who wrote the comic or even the writers of the show — very appropriate for Postmodernism) to appeal for a better ending, it might very well be just something what he wishes to happen for the monster and for himself. Which makes it more of a truly tear-jerking moment.
The last twenty minutes of "Emily".
"The Unnatural", baseball, fun-loving aliens, the gospel and song and finally It's just blood. The death of the alien who made such a good human is very heart-wrenching.
In "Monday", after Mulder was shot, Scully pleading with Bernard to let her leave with him. Made even more tear jerking because of the wounded look on her face, and the fact that she's near tears as she tries to stop Mulder's bleeding.