The X-Files's world is far from happy. Other than the deaths of too many good people thanks to the supernatural, twisted human beings or corrupt higher-ups, there is also the harsh returns to square one in Mulder's and Scully's pursuit for the truth.
- "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: I want to believe.
- Colonel Belt's suicide at the end of "Space". After having been tormented by a ghostly figure brought back from a Mars space trip, he throws himself out of a high hospital floor, plummeting to his death. His last thoughts are of his unmoving body floating in space after the ghost went into him on that day, meaning that he wasn't at peace with his final moments. At his funeral, NASA communications commander Michelle, who was someone who looked up to Colonel Belt, can only share a simple, teary nod with Mulder, another who admired that man. The last shot of the episode is a slow pan over the American flag draped over the Colonel's grave. It was just saddening to see an astronaut's passion flicker out and die throughout the episode.
- 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."
- "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.
- And earlier, when Roland locks himself in his room to get away from Tracy because he's having visions of strangling her. Poor Roland is terrified out of his mind, yet still frantic to protect her from himself. And Tracy, bless her heart, is crying too, able only to think it's something she did that's upset him.
- Deep Throat's death in "The Erlenmeyer Flask". He's shot in cold blood while bartering for Mulder's life, and dies in Scully's arms."Trust no one."
- Augustus Cole breaking down when Mulder corners him in "Sleepless". After spending an entire episode being a terrifying telepath wiping out all the people who were part of the experiment that caused him to lose his ability to sleep, he just starts crying and rambling about how tired he is. Even his last words are just "Goodnight".
- 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 Jerkass Woobie kind of way.
- 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 lets 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."
- In "Die Hand Die Verletzt", the main victim of the week, a high school student named Shannon Ausbury, is interviewed by Mulder and Scully. She almost immediately breaks down, tearfully discussing how her stepfather had repeatedly raped her and her sister throughout their childhood and that she's had three children sacrificed by the members of his cult upon birth. Thankfully none of this is true (even though Shannon genuinely believed it), but the shear thought of it is down-right traumatic. Even Scully can't help but hug the poor girl.
- Actually, some of it is. He father later admits that the cult does use children in the rituals, and that they use memory altering tricks to make them forget. In his words, her memories are being combined with things she heard on Geraldo.
- 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.
- 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 Nightmare Fuel, also tread into this territory. Teddy's in particular, for epitomizing every parent's Adult Fear. 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 Single Tear 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 Shoot the Shaggy Dog.
- The death of Mulder's father in "Anasazi", right after he had started to atone for his earlier work. His last words are to ask Mulder to forgive him for his mistakes.
- 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 Jack Black) 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 Driven to Suicide.
- 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 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 Scully's dog, 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 he 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 a 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 death of Owen Jarvis, a saintly, heroic, and selfless man who died as he lived, trying his best to protect Kevin.
- The death of Kevins mother, and his reaction to it.
- The murder of X in Herrenvolk, outed as the double agent within the Syndicate aiding Mulder and gunned down for it outside Mulder's apartment. He uses his final moments to direct Mulder to a new contact before dying. In spite of their brawling and arguing in the episode before it and others, Mulder is clearly saddened by the loss, and refers to him posthumously as having been a friend.
- "Memento Mori" is the episode where Scully's cancer is diagnosed. It is a direct and shameless heartstring-twister from start to finish.
- All of "Kaddish", especially the story behind the wedding ring. Poor couple, they could have been so happy together.
- Teager's backstory in "Unrequited". A US Soldier captured in Vietnam, left behind by the government and tortured by the NVA for decades. Who wouldnt be crazy after that? Even as he pursues his final assassination target at the Vietnam War Memorial, Teager pauses upon encountering a man he served with, and gives him a list of other American POWs still in captivity, begging him to make sure they are rescued. And as he lays dying of a gunshot wound beside the Memorial Wall, his final words are a recitation of his name, rank, and service serial number, as he no doubt repeated hundreds of times to his captors.
- "Musings of a Cigarette-Smoking Man", unreliable narrator aside, does little to dissuade the audience from believing that the CSM really does have little happiness in his life.
- Arguably, the biggest gut punch of the episode is when just after the CSM reads how his story was cut up, the man that sells him the magazine it's in wonders why anyone would read such a "piece of crap." The look on CSM's face says it all.
- The ending of "Elegy", with Scully crying alone in her car.
- In "Gethsemane", after having been told his quest is a lie and losing his proof of alien existence, the cherry on top is that those conspirators behind the aforementioned devastations gave Scully her terminal cancer only so he'd believe the lies they fed to him. The way they order those revelations, one could assume Scully's ailment was the tipping point of his suicidal thoughts.
- "Redux II":
- 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.
- Later, Mulder sobs at Scully's bedside while she sleeps.
- The ending to "Unusual Suspects". After the Lone Gunmen solidify into a trio, and go after the attempt to poison unsuspecting asthma patients with a mind control drug, things go to hell in short order - the warehouse is shot up, the drugs vanish, the trio are arrested, and the last they see of Suzanne Modeski is her being shoved into a car and kidnapped in broad daylight, leaving some harsh parting words. It's especially harsh on Byers, who saw every part of his worldview wrecked in the process."No matter how paranoid you are, you're not paranoid enough. Tell the truth. Reach as many people as you can with it. That's your weapon."
- The ending of "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 transition from Scully's laying with Emily to Emily's funeral is especially hard. The imagery of Scully laying with her dying daughter while the stained glass of the chapel portrays the Virgin Mary with her (living) son and Bill's newborn daughter in his wife's arms helps absolutely nothing.
- "The End" has one of the biggest downer endings ever. Not only is the X-Files shut down once more, CSM burns down Mulder's office out of spite. As soon as Mulder witnesses the wreckage, you would expect a breakdown of some sort, since he typically is the most emotional of the iconic duo. This doesn't happen. He can only have a Thousand-Yard Stare at his work and personal belongings now reduced to embers, while Scully hugs him, being on the verge of crying. The X-Files theme briefly and slowly plays on sombre horns, concluding the episode.
- "Tithonus": Alfred Fellig's Fate Worse than Death of living an endless existence, forgetting his wife's name and being unable to die, reaching hundreds of years old. His life is reduced to searching for people and taking pictures of the dead and dying, hoping for a glimpse of Death so he can finally die himself. In the end, he succeeds, trading his life for Scully's.
- "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.
- "Three of a Kind" opens and closes with them. In the first, is Byers's Tragic Dream. He's a Wide-Eyed Idealist and possibly the most moral man in that universe's canon. His dream is of a world where the country he loves lives up to the Type 1 Eagleland, where he has a comfortable middle class existence with the woman he loves and two adorable little daughters...but then it cuts to him standing in a vast desert, holding a wedding ring, all alone. And at the end? Well, Suzanne is safe and going off into a new life, but they'll likely never see one another again. And Byers is holding a wedding ring, out in the desert as she leaves.
- The ending of "Hungry":Rob Roberts: I can't be something I'm not.
- The end of "Closure", where Mulder finally comes to terms with Samantha's disappearance. The fact that this Moby song is playing in the background probably increases the sadness tenfold.
- The opening spoiler 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.
- 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 Monster of the Week in "Badlaa", which had taken the form of a child.
- Every scene displaying Scully's anguish in "This is Not Happening".
- At night, Scully and Skinner talk about the events of "Closure", where she thinks that Mulder will become starlight, like his sister was before him. Skinner's response is to try and stop her from thinking about the possibility of Mulder's death, because he still hopes for his survival. It's so much harsher when you know the outcome of this episode.
- Tears are in Scully's eyes when she tries to get Absalom to look at the folded picture of Mulder and tell her where he is. The search means a lot to her, because she cannot lose when she is so close to achieving this.
- The ending. Scully's search to find Mulder concludes when she is called over to his pale, lifeless body. She can only stroke his punctured cheek, with the realisation of his death hitting her hard. Cue her going into full denial mode and running to get Jeremiah Smith to heal him, only to be too late because of a UFO taking him away. When she realises this, she has a gigantic breakdown, yells out the episode title, and lets out one of the most emotional big "no"s EVER. Seeing her emotionally shattered compared to her usual stoic personality from earlier seasons, combined with her Not So Stoic moments in this season, hammers home how brutal and unflinchingly cruel her single goal turned out to be.
- Mulder's funeral in "Deadalive".Scully: He was the last. His father and mother... his sister... all gone. I think the real tragedy... is that for all of his pain and searching... the truth that he worked so hard to find was never truly revealed to him. (Starting to cry) I can't truly believe that I'm really standing here.
Skinner: I know. And I don't truly believe that... Mulder's the last.
- "Trust No 1", 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 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 one of the few times we ever see him cry.
- Doggett breaking down in "Audrey Pauley" begging the episode's namesake to go into the spirit world and have Reyes give them a sign she is alive.
- Reyes taking Doggett off life support in "4-D". Thankfully, it was a Doggett from a dimensional rift that was restored when he died.
- The end of "Jump the Shark" for fans of The Lone Gunmen with their deaths.
- The end of "William" when Scully breaks down over William's crib, realizing that she has to give him up to keep him safe.
- In "My Struggle", it's revealed that Mulder and Scully have broken up and become estranged, and both are now more or less completely alone.
- In "Founder's Mutation", Mulder and Scully discuss William, with Scully admitting that she hates herself for giving him up, while Mulder says that he's "put that behind [him]". Except it turns out Mulder hasn't put it behind him—both he and Scully still keep photos of William with them and fantasize about raising him.
- Said fantasies are themselves a mix of tearjerker and Nightmare Fuel. They start out happy and benign, only to get darker as Scully's and Mulder's personal fears take over. Scully's fantasy ends with William undergoing an alien mutation like Emily did, while Mulder's ends with William being abducted in exactly the manner Samantha was.
- Large portions of "Home Again", which deals with the heart attack and death of Margaret Scully.
- When Scully gets to the hospital, a nurse tells her that her mother was asking for "Charlie" (the youngest Scully child and who had apparently become estranged from Margaret). Not Bill (her favorite) and not Dana, not any of her grandchildren, but Charlie.
- Scully's speech to her unconscious mother:Scully: Hi Mom, it's me Dana. I'm here. I've been where you are. I know that Ahab is there, and Melissa. But I'm here, Mom. Bill Junior's here. And William - William's here. Please Mom, don't go home yet. I need you.
- Margaret's last words being to her missing grandson William, and Scully's reaction:Scully: (crying) Her last words to us were about our child, her grandchild, that we gave away. Why did she say that? Why did she have to say that?