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[[folder: Season 1 ]]

* "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 Mark Snow's score that really helps accentuate Mulder's loss. The sounds of the flute and synthesizer are gently building as we hear more of Mulder's recorded interview with a therapist.
-->'''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.
-->'''Therapist''': Do you believe the voice?
-->'''Mulder''': [[ArcWords I want to believe.]]
* 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.
* Scully's storyline in "Beyond the Sea" is heartbreaking, having her dealing with losing her beloved father. Especially her ending lines, "He was my father."


[[folder: Season 2 ]]

* Duane Barry, while far from the cuddliest of figures, is put through so much pain that one can't help but feel for him in a JerkAssWoobie kind of way.
* Whenever Scully breaks up and is NotSoStoic, 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."
* When Mulder thinks that he's lost Samantha again in "End Game", ''particularly'' for the scene where he confesses his mistake to his father. Mulder is uncharacteristically in tears while retelling what happened, and his father is nothing but cold, noting how negatively this will affect Fox's mother.
* In "End Game" when Mulder is knocked out by the bounty hunter and wakes up to find all of the clones missing, right after they had asked for his help.
* The deaths of several of the family members in "The Calusari", while primarily NightmareFuel, also tread into this territory. Teddy's in particular, for epitomizing every parent's AdultFear. Also, Steve's, due to Charlie shouting out for him while locked in the garage car, showing to us that the deaths are not entirely his doing.
* The final fate of Dr. Banton in "Soft Light", who, after spending the entire episode in torment and wishing for death so that he can avoid hurting others, ends up being used as a figure for experiments in a government research facility. He even can be seen letting out a SingleTear in the final shot of the episode. Additionally, Banton was forced to kill Detective Ryan before this (affecting Scully in a very hard way), which makes his ultimate ending a huge case of ShootTheShaggyDog.
* The death of [[spoiler: Mulder's father]] in the season finale, right after he had started [[TheAtoner to atone]] for his earlier work. His last words are to ask Mulder to forgive him for his mistakes.


[[folder: Season 3 ]]

* The end of "Paper Clip" -- Scully finds out her sister has died.
* "D.P.O." has a bit of this when we see Zero (played by JackBlack) begging for his life, just before getting blasted by Oswald's lightning.
* "Clyde Bruckman's Final Repose": Mr Bruckman's ultimate fate. After life seeing deaths, at times extremely gruesome, he felt DrivenToSuicide.
* From "2Shy", there's Jesse's reaction after realizing that her mother has been killed in Virgil Incanto's apartment. Further exemplified with her later discussion with Scully.
* "The Walk" deals both with the troubles that some Army veterans have trouble returning home from war (sometimes, if not often, feeling underserved by the Army that should ostensibly be helping them to recover). On the other side, several of Rappo's actions to take vengeance [[DisproportionateRetribution are pretty cruel]] , as seen with what happens to General Callahan's family.
* Much of the pain we see Skinner go through in "Avatar", from being accused of murdering a woman he slept with, to the conversations he shares with his estranged wife.
* The death of [[spoiler: Queequeg]] in "Quagmire". During the next scene, Scully is seen fighting back tears and barely listening to Mulder as he gives one of his exposition dumps. Made all the sadder, seeing as how [[spoiler: it was a parting gift from Clyde Bruckman, and she named it that because Scully's father often read ''Moby Dick'' to her as a child]].
* "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 LikeYouWouldReallyDoIt, his emotions are genuine.


[[folder: Season 4 ]]

* "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.


[[folder: Season 5 ]]

* 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".


[[folder: Season 6 ]]

* "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.


[[folder: Season 7 ]]

* The ending of "Hungry".
-->'''[[TragicVillain Rob Roberts]]:''' I can't be something that I'm not.
* The end of "Closure", where Mulder finally comes to terms with Samantha's disappearance. The fact that [[http://www.youtube.com/watch?v=ZFzogfFw-2Q this Moby song]] is playing in the background probably increases the sadness tenfold.
* The opening spoiler in "Closure" where Mulder talks about how desperately he wants to believe in some kind of afterlife and truth beyond this world that's known only to God.
* Scully breaking down and crying in "all things" as she feels that she doesn't know anymore what she wants in her life.


[[folder: Season 8 ]]

* The tear-jerking scenes from the "Within"/"Without" episodes, notably when Scully goes to Mulder's apartment, finds his shirt and falls asleep on his bed clutching it tightly.
* Scully and Skinner learning that Mulder was dying of brain cancer and hadn't told either of them.
* Scully's distress after shooting the MonsterOfTheWeek in "Badlaa", which had taken the form of [[spoiler:a child]].
* Scully's anguish in "This is Not Happening".
* Mulder's funeral in "Recap/TheXFilesS08E15DeadAlive".


[[folder: Season 9 ]]

* The episode "Trustno1", especially the e-mails between Mulder and Scully -- poor Mulder just wants to come home.
* The ending of "Release", with Doggett and his wife spreading [[spoiler: their son's]] ashes into the ocean.
* When Doggett's amnesia in "John Doe" gets broken by the memory of his murdered son. It's the only time we ever see him cry.
* The end of "Jump The Shark" for [[spoiler:fans of The Lone Gunmen with their deaths]].
* The end of "William" when Scully breaks down over [[spoiler:William's crib]] realising that she has to [[spoiler:give him up to keep him safe]].