One of the side effects of Cerebus Syndrome is that some gags from the early part of the story may no longer seem to fit the more serious tone of later portions. There is however a way to make these early funny elements consistent with the rest of the story: giving them a Cerebus Retcon. The Cerebus Retcon gives a rational, often cynical, In-Universe explanation or interpretation of early gags, frequently by giving them a late Deconstruction.
While this trope will frequently be the consequence of a RetCon, it may be hard to distinguish retcons that bring little alteration to the initial continuity from the author using the early gags as Foreshadowing of their serious explanation/interpretation, that can be part of The Reveal. This trope can hence cover both cases. For a trope in a similar situation, see Arc Welding, which sometimes overlaps with Cerebus Retcon.
Compare Reimagining The Artifact, Doing in the Wizard and Crapsaccharine World. See "Funny Aneurysm" Moment and Harsher in Hindsight, and Hilarious in Hindsight for an inversion.
Unmarked plot spoilers are abundant in this page, as the mere title of this trope is already suggestive. Tread carefully.
The destruction of F City in episode 22 was played straight (well, at least as straight as Excel Saga could ever get), with persistent effects spanning into the next three episodes. Before that, it had been destroyed at least twice and reset to normal by the next episode.
Another example: In episode 1, Il Palazzo shoots and kills Excel twice (the show's living Reset Button resurrects her each time). It's played for laughs. Him shooting her in episode 23, however, is played morbidly straight. It was serious this time because of the way she reacted, which was because he didn't just shoot her, he shot her and fired her. Plus the Reset Button had problems of her own at the moment.
Fullmetal Alchemist: Ed's short stature gets used for comic characterisation for most of the manga. Then it turns out he hasn't grown since the disastrous ritual because Al's body on the other side of the Gate is drawing nourishment from his to survive.
Medaka has a habit of copying everyone else's poses, as part of comic relief. After the Genre Shift, it's revealed she does this since she doesn't have her own identity.
Shiranui, among other things, is known for her incredible Big Eater tendencies, as well as a rather comical opposition to the title character. Turns out that she's Medaka's double, designed to help her from the shadows, eating more than she needs to, and having no true identity.
At some point in Love Hina, Ken Akamatsu must have realized that Keitaro was surviving in too many instances where he simply should not have. With the choice between toning down the girls' Comedic Sociopathy and simply hoping the fans chanted the MST3K Mantra, he made Keitaro's durability a part of the story, with at one point Kitsune ordering that it was alright to use lethal force while hurting him, as he was immortal. At a point where the manga became serious near the end, when Keitaro is dangling from a great height, he lets the audience know it's serious by even referencing his own ability to walk away from excessively violent slapstick injuries by saying that "at this height, I'll die, even if I'm immortal!"
The 6th movie starts out as the usual lighthearted ridiculous shenanigans, then slowly descends in to madness as you find out more and more about the island. Why do the inhabitants have leaves on their heads? Because they are fake representations created by a sentient "flower". Why does the Baron have the cute little flower on his shoulder? It's really the Lily Carnation, or a part of the Lily Carnation, which is a giant Eldritch Abomination that devours people whole. What about the funny short guy with the toothbrush mustache? He lost his True Companions to the Baron and the Lily Carnation, and has been in hiding on the island, trying to stop him.
Post-timeskip Sanji gets a major nosebleed every time he looks at a woman with Chopper making a mention that Sanji is using up his blood transfusions. When he arrives at Fishman Island where the mermaids were, he got a serious nosebleed and Chopper isn't able to help him because there were no blood transfusions left. Fortunately, they were able to find the right donor and he gets better. Cue the Okama who gave him the transfusion of blood, and one horrified Sanji.
Initially played straight with Nami's greed and distrust of pirates. Turns out her hometown was taken over by pirates, and she struck a deal with the leader to buy back the town from him if she could gather up enough money. Ultimately subverted, however, when the arc that deals with the pirates comes and goes, and she's still obsessed with treasure. She does, however, point out that all the money she steals is now hers to spend, and considering that she's had virtually no disposable income for virtually all of her life, it's easy to see why the prospect of adding to it appeals to her.
Inverted with Usopp's backstory. He initially started telling lies (especially about his father returning home) to keep his ill mother's strength up. But even after he had gotten over his mother's death, Usopp continued to lie out of habit.
One gag ends up turning serious very quickly, when Brook gets into a fight with Ryuma, who wants to cut off the former's afro. Brook turns out to be so defensive of his afro that the last time they fought, he agreed to leave Thriller Bark after his defeat if it would save it. Then it's revealed that the reason he's so desperate to hang on to his afro is because he wants Laboon to be able to recognize him when he returns to him, and since he's been reduced to a skeleton, the afro is the only part of him that's still recognizable.
Shinobu in Urusei Yatsura is an example. She starts out with the comedy ability to hit really hard when she gets angry. After a while, it becomes a real ability. The series never stops being a comedy, though oddly enough in movie 3 (Remember My Love) the aliens leave, and without the genre shift brought by the presence of aliens, Shinobu also loses the power.
Ah! My Goddess: Early chapters show "the system" preventing anyone from interfering with Keiichi and Belldandy's relationship. Chapter 285 gives this a rather dark spin. The system is also preventing their relationship from advancing, and it does so by altering Keiichi's feelings.
In Revolutionary Girl Utena the fact that Nanami gets constantly chased and/or attacked by all kinds of animals is hilarious, of course until The Reveal that Anthy whom Nanami constantly bullies is actually a witch and is strongly hinted that she cursed her because of it.
Similar to the One Piece reference above, Tamhome of Fushigi Yuugi was initially portrayed as a huge mercenary, even charging people for rescuing them. This is later revealed to be because he is giving the money to his huge, impoverished family. Once they've been slaughtered, he still makes reference to this trait.
In Pokémon Special, the first published chapter of the BW arc featured the wacky hijinks of Black's Tepig chasing a mischievous Zorua around Castelia City. Except that it turns out that this Zorua belongs to N and that he's being using it to spy on Black for ages.
In the comic version of Wanted, the supervillains use an actual, massive in-universe Cerebus Retcon in order to erase all memory of superheroes and supervillains. During this transformation, it shows in vivid detail how Golden Age visual styles and themes eventually shifted into a more realistic, Darker and Edgier style seen in more modern comics.
Batman R.I.P. and the events leading up to it are one big Cerebus Retcon. All that Silver Age Batman wackiness? All either hallucinations caused by Scarecrow or Joker gas, or delusions of a young Batman as he took part in a dangerous mental experiment to try to understand the Joker's mind.
Cassidy, hard-drinking roguish Irish vampire in Garth Ennis' Preacher, was a fun and charismatic guy. Then, later in the series, we got an uncompromising look at how pathetic, dangerous and destructive he genuinely was. Several moments you thought were simply gags and fun moments got a nasty pay-off. A joke where Cassidy says something "tastes like semen!" and then hurriedly tries to get out of suggesting he knows what that tastes like? He does know because he got so desperate for a heroin fix that he paid for it with oral sex.
Prior to Identity Crisis (and particularly during the Silver Age), heroes used "mindwipes" and other forms of selective memory erasure all the time, frequently to preserve the heroes' secret identities. Ethical issues relating to this were seldom (if ever) addressed. Suddenly, in Identity Crisis, the ethics of mindwiping came to the forefront, and were revealed as the cause of a major past schism in the Justice League.
In addition, several changes in the supervillain behavior were attributed to the effects of mindwiping. Most notably, this was used to explain how Dr. Light went from being a serious threat to the Silver Age Justice League to a joke villain constantly bested by the TeenTitans, by revealing that he was given, not just a mindwipe, but a personality aleration after an attempted rape in Identity Crisis.
The Trope Namer is Cerebus The Aardvark, which in later issues liked to go back and explain some of the more humorous characters and situations of the early issues as being much more serious than originally thought. For instance, a minor gag in the fourth issue was later retconned (over 180 issues later!) as having been a tremendously significant event which kicked off a chain reaction that changed the course of Cerebus's life and led directly to all his eventual misery. Had said gag not occurred, Cerebus would have actually ended up as ruler of the world.
Kid Eternity is a comic character from 1942. A clerk in heaven made an error and he died before his time while boating with his grandpa. He was resurrected to do good stuff by summoning heroes of the past. Then Grant Morrison got his hands on the poor kid in the modern age. Demons made up all that misfiling stuff. The clerk is a minor demon. The "historical figures" he becomes are demons as well. It's all The Plan about earning their way back into heaven by "helping" humanity via evilution. Oh, and he's an orphan; the man he calls "grandpa" is actually a child molester. Dammit, Morrison! At least the "revive dead people" part was retconned back in again. Kid Eternity is seen reviving Marvin. Who was killed by his dog. Who was really a demon. So, yeah. More Cerebus Retcon.
The Mad Hatter was always slightly creepier than most, but in the first Secret Six miniseries it became canon that he was a serial rapist, a drug addict, only ate food with hats on it, and was afflicted with macrocephaly. For a villain whose hat (harhar) is casual mind control and was drawn after a Tenniel illustration, this worked surprisingly well.
In the final Scott Pilgrim book, Scott leans from Kim that the very quirky flashback of book 2 wasn't very quirky at all. Basically he beat up the shy Chinese boyfriend of Kim, Simon Lee, to get with her, and to top it off, he told his best friend Lisa Miller that he was leaving and neglected to tell Kim so Lisa had to, even though Kim ended up shunning her for a month after that. Kim does admit that she was partially at fault for leaving Lee that easily though. It also turns out that all his quirky memory losses were part of Gideon's plot to mess up Scott.
John Dee, a.k.a. Dr. Destiny: originally a supervillain defeated by the Justice League, he had a magic ruby that could make dreams come to life. Sounds dangerous, but since this was The Silver Age of Comic Books, he was handily defeated and not thought of again for a long time. Come The Sandman, it was revealed that it was Dream's own ruby amulet, and that being kept in Arkham Asylum had caused Dee to go completely, omnicidally insane. When he stole the ruby back, he plunged the world into twenty-four hours of horrific madness straight out of nightmares and warped desires before finally being stopped by Dream's direct intervention.
Streetfighter: Chun Li has the death of Dan's father, Go Hibiki. Depictions of Go Hibiki's death have been comical, showing how Dan is a stereotypical character with a generic backstory. In this comic... it's played completely straight. Dan's father is murdered by Sagat and he's left traumatized.
Funky Winkerbean did this as part of its descent into Cerebus Syndrome. For starters, the once humorous bullying of Bull Bushka against hapless nerd Les Moore was revealed to be the result of an abusive parent after the first time skip.
In the Jackie Chan Adventures fic Queen Of All Oni, after Jade becomes evil once more, we see that her parents neglected her almost to the point of abuse, painting her being sent to live with Jackie in a new light. In fact, she herself says that before her Start of Darkness, she would have thought being sent to Jackie's as the best thing that ever happened to her.
There is an entire genre of fanfic called angstfic, which makes the characters wallow in angst — especially if the original fic that the fanfic is based on is a wacky comedy or lighthearted. The usual victims are Pokémon and any comedy by Rumiko Takahashi.
In one Magical Girl Lyrical Nanoha fanfic titled Behind the Smile, it is suggested that Hayate suffered sexual abuse in the foster care system before living alone, and her Skinship Grope tendencies were a way of warding off unwanted male attention.
In Crumbling Masks, a Zero No Tsukaima fanfiction, Saito and Louise relationship of Abuse Is Okay When It Is Female on Male is taken seriously; but instead of the usual angst one might expect from this type of stories, it ends with both of them realizing they actually enjoy being in a S&M relationship and accepting themselves as the kind of persons who would enjoy that kind of thing.
Many, many Naruto fanfics turn Naruto's status as village black sheep into outright hatred and open, often homicidal abuse. So, that scene in the beginning where he's getting chased for vandalism by the equivalent of the Keystone Kops? People are actually trying to kill him over it. The small apartment he lives in by himself? A slum with no hot water that people frequently vandalize. His birthday? A festival in memory of the survivors of the Fox's attack on the day he was born, where he must fear for his life. The Hokage's advisors? Part of a village council made up of clan leaders (a.k.a. the parents of all his friends) who want nothing more than to exile him or publicly execute him. His favorite ramen stand? The only place in the village willing to sell him food. Yeesh.
Films — Animation
Probably the quickest one in history is towards the end of the original The Land Before Time movie — which is also something of an in-universe example. Cera screams for help when what appears to be some sort of tar monster approaches and picks her up, only for Ducky to reveal -after Cera's fit of panic, of course- that it is herself and their friends covered in tar. Cera irritably pries herself free, squeals as she falls to the ground, and defensively claims that she knew it was them the whole time. The others laugh rather mockingly at Cera, (who, up to this point, has been boastful and overly-proud) which continues as she slips in tar and bumps into things in a comic way, as she marches out of the cave. Cut to her alone outside of the cave, where her facade finally breaks and she begins to cry.
In Lilo & Stitch, when Lilo's home gets destroyed by a bunch of aliens, it's played for laughs. When Nani and social worker Cobra Bubbles come back (just after Nani was able to convince him NOT to separate her from Lilo)... it leads to the social worker deciding to take the little girl away, much to Nani and Lilo's despair.
Along the same lines, it's hard to not laugh when a young Hercules accidentally sets off a Disaster Dominoes that destroys an entire agora. But when the understandably upset townspeople proceed to yell at and insult the poor guy...
Near the beginning of The Aristocats, the evil butler kidnaps the title cats so he can leave them all for dead in the French countryside. However, in the process he is attacked by a pair of dogs leading to an entire three minutes of slapstick. When the butler finally escapes the two dogs, we find out that the basket containing the cats fell out of the butler's motorcycle while the dogs were still attacking him, and the cats immediately realize upon waking up that they are all no longer with their owner, and at the same time, said owner goes crazy when she finds out that her cats are gone.
Films — Live-Action
In Superman II, Zod's Dragon Non was a silentbrute upon whom Jor-El looked with contempt. This characterization carried over to the comics... and then it was revealed Non was once a close friend of Jor-El's until he was abducted and lobotomized.
In the first Star Wars film A New Hope, Luke Skywalker's Aunt Beru notes to his Uncle Owen "Luke's just not a farmer, Owen. He has too much of his father in him.", to which Owen says "That's what I'm afraid of." In The Empire Strikes Back, we learn that Luke's father is, in fact, Darth Vader, one of the most evil men in the galaxy. And it's even worse if you consider the Prequel Trilogy, as we see in Attack Of The Clones, shortly after Anakin originally met Owen, he went on a rampage, slaughtering dozens of Sand People after his mother's death by their hands. It goes from mere apprehension that Luke might get himself killed to fears that Luke might turn evil. One of the things Darth Vader is best known for in the Original Trilogy is Force-choking anyone who angers him. This gets very tragic in Revenge Of The Sith, as the first person Anakin/Vader used the Force choke on was Padme, the love of his life, and the reason he joined the Dark Side.
In the first two Men In Black films, K was The Stoic, though this was mostly played for laughs. When Boris the Animal goes back in time in the third film to kill K, J goes back to save him, and finds that K is a likable person with emotion. The reason K has always been such a curmudgeonly old guy is because he witnessed J's father sacrificing himself to save K from Boris back in 1969, which ended up with K somewhat becoming a surrogate father to J.
In the movie Zombieland, Tallahasse's beloved dead puppy turns out to be his only son.
In The Avengers, Tony's flight through the Chitauri wormhole at the climax of the movie is just a good old fashioned fist-pumping action climax, and his resultant brush with death (which he obviously survives) is Played for Laughs, with Tony absentmindedly rambling about going to get shawarma immediately upon waking up. But then Iron Man 3 reveals that he actually got PTSD from the experience, and a minor plot point in the film involves him struggling to cope with anxiety attacks following the battle in New York.
At one point in The Hitchhiker's Guide to the Galaxy, a Million to One Chance produced when Arthur Dent accidentally activates the Infinite Improbability Drive causes two missiles to be transformed into a sperm whale and a bowl of petunias, which fall onto the surface of an alien planet. While the whale contemplates its brief existence at some length before its demise, all that the bowl of petunias thinks is, "Oh no, not again." This thought is left unexplained, with the comment: "If we knew exactly why the bowl of petunias had thought that we would know a lot more about the nature of the Universe than we do now." The bowl of petunias, however, is dismayingly explained in Life, the Universe, and Everything as being one of many incarnations through time and space of a creature called Agrajag, whom Arthur Dent killed in each form (also counts as a Brick Joke).
Mostly Harmless reveals the entire truth: The Guide Mark II somehow used Reverse Temporal Engineering to screw with Agrajag's reincarnations so that Arthur would be brought to the Cathedral of Hate before he ducked an assassin's gunshot at Stavromula Beta. This is not a paradox, although it does ensure Arthur's eventual arrival. The Guide's purpose in this was simply to ensure all remaining humans (Arthur, Trillian, Tricia, and Random) were back on Earth before it was demolished again, this time for good, by the Vogons.
Stephen King's story The Library Policeman starts off goofy and turns deathly serious, casting the earlier goofy parts in a new light. This reflects the very writing process of the story: King started off writing a goofy tale and found it turning into a deathly serious one, so he took it and ran with it.
The Courtship Of Princess Leia had a rather stock villain duo in Warlord Zsinj and General Melvar, dim-witted and eeeheeheeeeevil sadistic bad guys who had the resources — a Super Star Destroyer and a device that cut off the sunlight from a particular planet — to threaten our heroes. Their resources were more of a plot point than they were; the only role they played was to leer menacingly and set up those things, then be killed quickly. In the X-Wing Series, set earlier, Aaron Allston made it a point to expand on those two, making them Faux Affably Evil, very intelligent, and quite essential to the plot. Their two-dimensional idiocy became Obfuscating Stupidity, and they actually turned into legitimate (and very entertaining) threats.
Hermione's attitude towards House Elves in the series was always treated as your average tree-hugging annoyance. Especially in regards to Kreacher as Sirius would crack sarcastic jokes about Kreacher obsessing over the family members' old belongings and even making death jokes about him which Harry and Ron openly laughed about. Then in the final book and we find out exactly what Kreacher has been through... Sirius's jokes and attitude don't seem so funny anymore.
A more notable example would be the way a Defence Against the Dark Arts teacher never stays on for more than a year, to the point where people joke about the position being cursed. Turns out, it is: Voldemort himself wanted the position many years ago, but Dumbledore refused to give it to him. (Obviously, this was before he became known as wizard-Hitler.) Ever since, no one has been able to hold the job for more than a year without something happening to them.
Neville Longbottom is bumbling and forgetful, and most of the other characters (especially Snape) tease him for his incompetence while his grandmother relentlessly pushes him. We later learn that Neville's parents were Aurors that were tortured into total insanity, a significant part of his bumbling lack of self-esteem is fear of not living up to their example, and his grandmother's nature was to toughen him up to protect him from the same fate.
In Sorcerer's Stone, Hagrid is presented as a goofy, over-sized character who is clumsy with his magic and hides his wand in an umbrella. This is presented as simple comic relief. It is later revealed that Hagrid is a half-giant and has been suffering from Fantastic Racism his whole life. He is clumsy with magic because he was framed for Tom Riddle murdering Moaning Myrtle, and was expelled from Hogwarts early in his education. Accordingly, he has to keep his wand in an umbrella not to maintain The Masquerade, but because he's not allowed to have a wand in the first place.
J.R.R. Tolkien did this with The Hobbit. Bilbo recovers a magic ring from Gollum's cave after winning a riddle contest. While the original story did make plain that Bilbo was riddling for his life, the ring he retrieves is later treated as a precious prize, saving his life several times and leading to his happy ending. Years later, when it was time to release The Lord of the Rings, Tolkien retconned the story (actually rewritingThe Hobbit) to tie in with the fact that the Ring is in fact a malicious artifact made of pure evil that was using Bilbo to escape Gollum's ownership. The existence of the first edition of The Hobbit was even deconstructed: it records Bilbo's lies about how he got the Ring and what it was like.
In Sharon Creech's The Wanderer thirteen years old girl Sophie tells a couple of stories about her grandfather Bompie. Most stories end with Bompie ending in the water, where "he was frightened, was nearly pulled under, had to struggle hard and long to get out, after which his father gave him a whipping and his mother gave him a pie", which at that moment was more funny than actually scary. But in the end of the book, we learn that this ending is imagined by Sophie. When she was four, her family was caught by a storm during sailing, their boat sunk, her parents died and she had to swim hours to reach the shore, all alone. For her, this wasn't funny, it was her Primal Fear
Catch Twenty Two: In which Captain "Aarfy" Aardvark constantly brags about having never paid for sex, but is later revealed that this is because he forces himself upon and often rapes women.
Though not a comedy, Bones managed this. Booth's increasing tendency to receive advice from famous people during dreams turns out to be caused by brain cancer that's slowly killing him.
Billy on Ally Mc Beal got a hugely out-of-character haircut, became comically misogynistic, and started seeing amazing, wacky things everywhere. Like Booth in the Bones example above, Billy had a brain tumor. Unlike Booth, he was Killed Off for Real.
When we're first introduced to Dr. Bashir, it's played for laughs that he's incredibly young and arrogant about what a great doctor he is. But it gets distinctly weird to look back on this after a fifth season episode reveals Bashir's intelligence is the result of illegal genetic enhancements that were performed on him as a child. It's even vaguely implied that prior to the procedure, he had some degree of outright mental handicap. Fortunately, it was well-established that Bashir always used his full, gene-enhanced intelligence on any medical/important problem.
In a more minor example, in a early episode, Bashir mentions out that he confused a pre-ganglionic fiber with a post-ganglionic nerve during his medical finals. When fans pointed out that this is a mistake that no competent medical student would make, the explanation was retconned that he got the question wrong on purpose to avoid being valedictorian. This is later retconned further to explain that he wanted to avoid showing his full abilities to disguise his genetically-engineered background.
In Star Trek: The Next Generation, resident Proud Warrior Race Guy Worf makes an offhand comment about having a poor sex life due to most human women being physically fragile compared to him, lacking his Klingon physiology, meaning he has to restrain himself too much to enjoy sex. This same issue is later referred to in a much more dramatic fashion in Deep Space Nine, when he explains that as a boy, he accidentally killed another boy during a football/soccer match when their heads collided, which lead to his restrained and uptight demeanor as he feels he must always be careful to avoid harming other, more fragile beings. It also became relevant when he married Jadzia Dax, and she was constantly in Dr. Bashir's office for broken ribs. As was Worf. Not that they minded.
Power Rangers RPM got gags out of Doctor K not going outside and her mention of growing up in Alphabet Soup, only to then reveal the utter horror of what Alphabet Soup did to her.
It isn't exactly comedy, but the subplot in the first episode of Heroes about Angela Petrelli getting arrested for shoplifting socks and her sons bailing her out is certainly pretty lighthearted. That is, until Volume 4 rolls around. In the episode 1961, we learn that Angela had a sister who she left when she was a child, regretting it ever since. We also learn that whenever she finds herself missing her sister particularly bad, she, you guessed it, steals socks. Suddenly, that lighthearted moment in the series premier seems a lot more disturbing.
Sometimes, a Cerebus Retcon happens naturally as the result of Character Development over a series. For example, Wesley was a one-note bumbling Upper Class Twit when he first appeared on Buffy the Vampire Slayer, completely played for laughs. Once he became one of the regular cast of Angel his character was fleshed out enough to reveal that his early awkwardness was largely the result of a painful childhood with an abusive father; throughout the series any mention of his father causes Wesley to momentarily revert back to his old bumbling. His father's visit in "Lineage" is an especially dark example. This being Season 5, Wes has become extremely badass (seriously, he'd have a chance against a top of his game Ripper at this point). Finally he has to shoot his father to save Fred's life. Luckily, it was a robot.
Angel also applies a massive Cerebus Retcon in Season 4 in an attempt to inflate the season's Big Bad. The minor and previously played-for-laughs character Skip not only takes a hard turn in going from comedy to drama, but in one speech gives exposition about how the entire series up until that point has been orchestrated by the mystery newcomer: Though the speech does not factually contradict the storyline, it indicates a premeditated arc with every event previous to the speech for all main characters as well as the speaker itself which clearly had not existed in the story's mythos.
"You have any concept of how many lines have to intersect in order for a thing like this to play out? How many events have to be nudged in just the right direction: Leaving Pylea*
Lorne heard music in his head all his life (which doesn't even exist in his universe, so he thought he was going mad). A portal accidentally transported him to Earth, where he discovered music and set up a neutral turf karaoke bar which became a lifeline for Angel's Investigations.
, your sister*
Gunn's sister was turned into a vampire which he was forced to kill which ended up helping him cross paths with, and bond with, Angel.
, opening the wrong book*
Fred left home for a specific university, took a part-time job as a librarian and just happened to open a book she was tidying away that transported her to Pylea - the same portal that dragged Lorne to Earth, in fact.
, sleeping with the enemy*
Wesley and Lilah, which caused a lot of team conflict but also directly led to the discovery Earth occult books had been doctored to remove evidence of the Big Bad because Lilah was willing to share her pan-dimensional versions with Wesley, which turned out to be undoctored. This was a major clue against The Beast.
In Glee, Terri's increasingly erratic behaviour in the first series caused the character to get severe backlash, particularly from the fake-pregnancy storyline. In the second series, it's revealed that her therapist had put her on strong medication, implying that she likely suffers from severe manic-depression.
Tina Cohen Chang's buttmonkey status in season 2 was played for laugh when we were meant to laugh at her getting hysterical during a rare solo, and her getting booed off stage in another episode when she worked on the performance for a week and cried about it for a month. This was apparently, hilarious (Her fans disagreed). In season 3, after the strong backlash fans had against her getting neglected, Cohen Chang got her own cerebus retcon episode (Props) in which the glee club is made to feel guilty about her lack of solos, lines or appreciation.
Subverted, as by the end of the episode she decides she was being "selfish" and that "Rachel Berry is a star" (to quote her freakin' BOYFRIEND), and apoligises for the retcon.
In Farscape, originally Crichton was merely hallucinating Scorpius in the episode "Crackers Don't Matter", being driven mad like everyone else. The writer's liked the idea of an invisible Scorpius acting as the devil on Crichton's shoulder so much, they retconned things so that the hallucination was actually due a neural-chip implanted by Scorpius in a previous episode, eventually dubbed "Harvey".
Merlin had a plot where Arthur ended up falling for Lady Vivian thanks to a love potion and Merlin mistaking his lovestruck ramblings for talking about Guinevere. This leads to a funny sitcom style mix up which then becomes instantly not funny when we see Gwen waiting anxiously for Arthur to meet her on a date when he's actually going to see Lady Vivian.
An episode of Raising Dad has Sarah become insecure about her nose and everyone's teasing is Played for Laughs. However she considers getting a nose job. Emily constantly drops jokes about Sarah's nose but then she hears what actually happens in cosmetic surgery and is horrified that Sarah wants to do that to herself.
On TV Tropes, many Wild Mass Guessing entries for comedic or children's series fall into this, as they take an amusing character or location and go on to speculate that said character is a Time Lord, is slowly starving to death while trying to stay sane while imagining the rest of the series, or is suffering from PTSD.
Plenty of things from Warhammer 40000 when it became more serious after the silly first edition. Eldar lived on Craftworlds and had a boring life because they were retreating from Slaanesh and if you aren't disciplined he would devour your soul. The Emperor, originally implied to have been confined to the Golden Throne because of old age, had to be put on life support after a duel with his most beloved son.
In Bionicle, the traitor Metus got turned into a snake and banished to the wastelands. The DVD for the movie The Legend Reborn included a short, comedicbonus cartoon that Homaged the classic Wile E Coyote And The Roadrunner and Tom And Jerry cartoons, in which he attempts to drop a boulder on the heroes, but Team Pet Click foils his plans and his army of Scarabax beetles make short work of the snake. Metus's desperation is played entirely for laughs. Later, when other characters came across the snake Metus out in the desert, we found out he had survived all this time by eating rats, and was also suffering from a fatal mental disease that made him unable to dream (and thus, according to the story, release his stress), so he outright begs them to kill him, because he just couldn't take it anymore. Lucky for him, he later regained his ability to dream and his transformation has also become undone.
The Darkness Beyond Time from Chrono Cross in relation to the time travel from Chrono Trigger. Basically all discarded timelines are dropped into the area. So for example, the people from the Lavos destroyed future are down there.
In The Legend of Zelda: A Link to the Past, players are introduced to the dark world via Link turning into an adorable bunny. Then it becomes apparent that almost all of the other people stuck there have transformed into monsters or even trees. One of the most tragic examples is the guy whose father asks Link to look for, and after you find him, he gives you his Ocarina and turns into a tree, permanently... until you destroy Ganon, then he gets better.
In the original game, Metal Gear, Snake looked to be in his twenties - but he looked to be late-middle-aged in Metal Gear 2 Solid Snake. For the sequel Metal Gear Solid, the character designer decided to go with a Solid Snake who appeared to be in his early-thirties, younger-looking than his previous incarnation. As a joke referencing this, the characters who knew Snake in Metal Gear 2 joke about his 'age'; the sign that Gray Fox is back to normal is when he teases Snake with the throwaway line "You haven't aged well". However, in Metal Gear Solid 2, which started the Patriots plot arc, Snake is explicitly mentioned in the script as looking almost unrecognisably older than his self in Metal Gear Solid, even though MGS2 starts only two years later. Liquid spells it out:
"You're drowning in time! I know what it's like, Brother. Few more years and you'll be another dead clone of the old man!"
And it continues in Metal Gear Solid 4. The reason for the Plot-Relevant Age-Up was changed to fit in with Retcons introduced in the third game, but becomes entirely horrible. Snake now appears to be in his mid-to-late seventies and his health is suffering as a result. His own parents look younger than he does. It's very alarming to remember that the whole plot element started as a Continuity Nod joke.
Knowing the developer, it was probably intentional that the gameplay obstacle before fighting the final bosses of Metal Gear and Metal Gear Solid 4 was the same — a linear area which damages Snake as he crosses it, and there's no way he can prevent it sapping his health. In Metal Gear, you were told by one of the support characters to eat Rations (which immediately restored your health bar) in order to get across the electric floor. In Metal Gear Solid 4 — we'd rather not think about it.
Applying Broad Strokes to Metal Gear and Metal Gear 2: Solid Snake allowed their eight-bit wackiness to be taken fairly seriously in the Solid series. Snake didn't seem that affected by the events of Outer Heaven at the time (he also had to do things like avoid giant constantly moving rolling pins and use a bomb blast suit to make himself immune to a strong wind), and Metal Gear 2 attempted to paint him as a very traditional action hero who retired after Outer Heaven because he was a loose cannon and too badass to take orders from authority. Metal Gear Solid, and its Alternate Universe counterpart, Metal Gear Ghost Babel, claimed that Snake suffered immense guilt over his actions in Outer Heaven, got diagnosed with PTSD, and was forced to retire and go into hiding because he was unable to cope with the demands of everyday life.
One scene in Metal Gear 2: Solid Snake involved Snake knowing a woman for all of five minutes. She tells him about her family's history, asks him about his (he says "I have no family"), and then she dies. Snake's over-the-top grief at her death was, at the time, a major Narm. In Metal Gear Solid, which established that Snake had been essentially growing up in near-total isolation and had never had anyone tell him about their life or ask him about his own, his instant attachment to her seems very justifiable and deeply tragic.
The reason why The Patriot in Metal Gear Solid 3 Snake Eater, a copy of The Boss's Weapon of Choice, has infinite ammo, is that it has an infinity-symbol shaped drum magazine, giving infinite ammo. However, in Metal Gear Solid Peace Walker, it's explained that the Patriot has infinite ammo because "they say The Boss left a part of her soul behind inside it", making it more into a blessed memento of a supernaturally-gifted soldier rather than a cheap joke. It winds up a Voodoo Shark though, as the infinite ammo is explicitly noted about it before this could have happened. You only get the Patriot after you have killed The Boss, but when talking about it Snake had not yet killed his mentor, and the method that Snake gets it is lampshaded for being dubious. He isn't even supposed to have it until after he kills The Boss.
The Ratman's Companion Cube-related scrawlings in the first game are amusing (if a bit unsettling) because it's hard to imagine what sort of person would be that attached to an inanimate box. The Lab Rattie-in comic reveals that Doug Rattmann was a formerly medicated schizophrenic, that his Companion Cube really was his only friend, and that he ultimately sacrificed everything to save Chell's life.
The Big BadGLaDOS has a hysterical black comedy streak a mile wide. In the finale, you disassemble her cores (who are also individually hilarious) and destroy her. In the sequel, not only do you learn that GLaDOS has been reliving that "death" millions of times since you killed her (though you only have her word on this), but also that Aperture Science was killing people for decades before you came along, Chell has been trapped in the facility since she was a pre-teen, GLaDOS was made by uploading Cave Johnson's secretary (in the deleted content it's clear this was against her will), and that the facility has thousands of other test subjects to be tormented and murdered.
Portal 2 has Wheatley invoke this; at the beginning of the game, he falls off his rail comedically (it's impossible for the player to catch him). Post-Face Heel Turn, he mentions his grief at you "purposefully" failing to catch him during his rant during the Final Boss fight.
During the game, GLaDOS repeatedly mocks Chell for being an orphan. Considering she also mocks Chell for a lot of things which aren't true, it gets lost in the shuffle. In the sequel, it's revealed that Chell was the daughter of an Aperture Science researcher and that GLaDOS' massacre happened on "Bring Your Daughter to Work" day. Chell is indeed an orphan because GLaDOS murdered her parents (possibly in front of her eyes) and has been rubbing it in her face the whole time.
In Half-Life, there are only about 3 scientist models and several of them die in ways which are intended to be comic. In Half-Life 2, each of those models has been given a specific name and arc. One has become The Quisling leader of humanity. One dies horribly at the end of Episode 2 in a very dramatic scene. Curiously the third remains the comic relief, however.
Billy Vs Snakeman has a New Game Plus method called "looping". Originally it's just treated as your character being signed on for a new season of a TV show. Then it's revealed that this is the result of a series of time-manipulating experiments, dating back to a massive war against Kaiju that caused horrible damage to the world. And it's just the first of several revelations.
In Tales Of The Abyss, Guy's gynophobia is a side effect of his childhood trauma. Namely, being trapped under the corpes of his entire female household.
Intentionally invoked in Persona 4. Try looking at Adachi as the Bumbling Sidekick after finding out who the killer is. His odd moments of talking out loud about the murders when the gang is around suddenly makes more logical and darker sense.... Along with this, all of the party member's attitudes are revealed to be the cause of their major issues, like Kanji's homosexuality complex and Naoto's gender complex. Kanji's earlier comedic outbursts come off as tragic by that point.
Deadly Premonition uses many of its odd gags and bizarre humor for foreshadowing—everything from the idiosyncratic behaviors of the main character to some of the throwaway joke lines end up hinting at the true nature of what's going on. But one of the biggest examples involves a certain tattoo—in an early comedic scene, it's revealed that Thomas has an Embarrassing Tattoo, which protagonist York chuckles about and shrugs off: "We all lived through the 80's." Except the tattoo is actually a symbol of his fanatical devotion to the sheriff, who has been drugging him with red seeds and trying to frame him for the murders he committed. A devotion that gets even worse due to the insanity-inducing purple fog, which poor Thomas is especially susceptible to.
Dr. Eggman in the Sonic the Hedgehog franchise was a typical evil cartoon villain that wanted to take over the world in the most obscure way, which was capturing animals and turning them into robots that would do his bidding. By the time Sonic Adventure came to be, Dr. Eggman took a more dark approach to his evil schemes, such as trying to control a god with unlimited power and then deciding to fire a missile at a city when he fails in his original plan. Dr. Eggman even takes control of a weaponized space colony and fires a laser at the moon, cutting it in half! And that was only a warning shot! Dr. Eggman's darker persona stayed with him for a while although Sega attempted to dial it back a bit by making Eggman a bit more cartoonish for the narm factor, which can be seen in Sonic Colors and Sonic Generations. Dr. Eggman does return to his roots with animal capturing in Sonic the Hedgehog 4 as a throwback to the classic games.
In the first Ace Attorney game, many people are surprised that Manfred von Karma was only penalized when he presented forged evidence in court. Even by the standards of the ridiculously unfair justice system of the series, this seems odd, since come Apollo Justice Phoenix was fired for doing the same. Then, in Investigations 2, you learn that the reason von Karma only got off with a penalty was because the (at the time) chief prosecutor was just as corrupt as he was, and was in on the forgery.
A lot are done in Hatoful Boyfriend's BBL route. Highlights include — Oko San isn't just an idiot, he's an older breed of birds that is less Uplifted than the others; Anghel isn't actually a fallen angel but has the ability to induce hallucinations in others; Ryouta's weak stomach and Oko San's insane speed are due to Shuu testing drugs on them; Nageki didn't actually kill himself by jumping from the library window due to being bullied (as was implied) but burned himself to death in an underground laboratory beneath the library to prevent himself being used as a biological weapon; and Kazuaki isn't just obsessively mourning the loss of the bird in the blacked-out photo, but is pursuing a Machiavellian Revenge scheme in his name.
In Rewrite Chihiya, Kotori, and Lucia's routes end fairly happily considering most of humanity is still alive. However the Terra route reveals that in the end the earth eventually dies taking humanity with it due to salvation taking place.
Maji De Watashi Ni Koi Shinasai: Most scenes involving Touma, Jun, and Koyuki after clearing the Ryuuzetsuran path. Most notably, the ending of Chris's route is the only one where Touma opts not to continue in their family's line of work and instead decides to "live for love", a choice that the Ryuuzetsuran route's reveals really puts into perspective.
Early parts of A Profile joke about Masayuki's unathletic physique and easily running out of breath while running to school. But then it turns out he's so weak because he collapsed due to a hole in his lung and was hospitalized for a long time, leading him to become completely out of shape and ruining his love of the track field. After this, the jokes largely vanish.
In Umineko No Naku Koro Ni, Jessica Megaton Punches one of her friends at school with a brass knuckle after being pissed off in Turn of the Golden Witch. This stance is seen as a joke. Later, in Alliance of the Golden Witch, she uses the brass knuckles again and they suddenly become conducts for Supernatural Martial Arts.
The pointless fighting between the Reds and Blues for control of a box canyon? Just part of a live-fire simulation for the Freelancers to train in, and everyone else involved is a scrub soldier chosen for their expendability.
An early Running Gag is Grif forgetting or losing track of Red Team's ammo. Reconstruction reveals that he's been selling it to the other team, and when some other Red soldiers find out they put him up in front of a firing squad.
O'Malley and Gary were two evil AIs who by and large were ineffectual and comedic villains. The flashback episodes to their time in Project Freelancer, however, play Omega's violent and hateful threats, and Gamma's deceptiveness much more seriously. They even help torture a fellow AI.
The last chapters of Reconstruction loosed a whole barrage of these. Church getting killed, becoming a ghost, and possessing a robot body? There's no such thing as ghosts, he's an AI. Not feeling anything when Omega possessed him, always agreeing with Delta? Church is the Alpha AI all the others came from, because he was tortured to the point of amnesia. His girlfriend Tex, who always seems to fail just when she's about to succeed? She's an AI too, based on the memory of the original Dr. Leonard Church's loved one, and will always fail because that's what he remembered the most about her. And that original Dr. Church was the template of the Alpha-Church AI.
The finale of Season 10 turns the last forty episodes on their head. Agent Carolina's bitter rivalry with Agent Texas for the esteem of the Director of Project Freelancer? She's the Director's daughter, meaning she's been unknowingly struggling against a copy of her mother the entire time. While the Director watched.
Faye getting drunk starts out as just an excuse for her to talk with a Southern accent and engage in wacky hijinks, but it later becomes a plot point that she's an alcoholic due to trauma in her past.
Also, Hannelore's rather unusual quirkiness and OCD in her early appearances are explained in much later comics as being an incredible improvement over her near paralytic insanity during her early childhood.
The Goo started out as a Freak Lab Accident, but returned in the "Sister" arc, revealed to be driven by a device sent by Tedd's alternate-dimension duplicate to kill him.
Furthermore, a gag character, the Demonic Duck, originally appeared as a one-shot gag when people would need a distraction and then point out his appearance, the joke being that the duck actually being there was far more ridiculous than someone using such a specific distraction. The duck turns out to be an actual character with dramatic effects on the plot later.
Not to mention the Hammerchlorians storyline — a simple, running joke gone supernova. Not only did he explain the joke (Star Wars reference, anyone?), but he wound up putting an immortal, extremely powerful entity in a main character's debt, and giving her new spells and an angst-splosion to boot.
There are a lot of subtle examples of this in EGS as it moved from a wacky tone to a more serious one. A simple example is Sarah wearing a beret as part of a visual gag early on, and then a later strip showing a serious explanation on how she got that beret.
Riff, an amateur Mad Scientist and "freelance bum", routinely invents pieces of advanced technology such as dimensional portals, giant robots, and ray guns. Originally there was little mention of where he got the materials to build these devices, even though he seemed to have no source of income. However, in a later story arc, Riff reveals that he was actually a freelance inventor for the villainous Hereti Corporation, who gave him a salary and a sizable expense account in exchange for the blueprints to all his inventions. After Riff rebelled against Hereti Corp, he lost access to their resources. While he still creates ridiculously powerful and dangerous devices, he hasn't been able to do so nearly as frequently after the Dangerous Days arc, and (much to his horror) has had to get a regular job in order to pay the bills. He still bemoans the fact that he can't afford as much cool stuff as he used to, wailing, "I used to have a budget!"
Similarly, in the early "vampire" story arc, one of Valerie's vampire compatriots asks her why she has a crush on Torg, upon which she has a flashback to her pre-vampirism husband, a double of Torg, accidentally impaling himself on his own lance. Cue the Stormbreaker Saga, when Torg is stranded in the Dark Ages and his attempts to save Valerie from becoming a vampire are played for drama. In the end, after Torg goes back to the present, Valerie's husband dies in the accident, and it is revealed that this tragedy made her decide to join the vampire circle. Also retconned the accident from being the clumsy mistake expected of Torg to the result of recovery from a debilitating curse, in a character who was otherwise a competent warlord.
Dave isn't exempt either. Early on, it's mentioned in a throwaway gag that he's deathly allergic to bee stings. Years later, in the Adversary storyline (which is pretty much solely responsible for tossing the comic into Darker and Edgier territory), as he and Margaret are running away from the Devil, they find that their path leads through a field of sunflowers... and bees.
The protagonists discover at one point that before dying their old company doctor created a modified cryogenic kit capable of providing illegal and extreme modifications and performing far more powerful reconstructive surgery than a normal kit should. Initially this is just an excuse to solve the fact that almost the entire main cast were reduced to heads in jars at that moment, but later they run into a bounty hunter hunting down said doctor and we discover that a massive government conspiracy is built around "Project Laz-R-Us" and the attempt to make humans effectively immortal, and certain government agents who discover that the protagonists know about it want them dead.
Something similar happens with Petey, initially a high-level warship A.I. with issues about ghosts. Eventually, he becomes a nigh-omnipotent nascent A.I. god by fusing with virtually every other A.I. in the galaxy in a bid to prevent the galaxy's annihilation, and then sets out to subvert and dominate every other galactic power to build a power base big enough to fund and supply a genocidal assault on the Andromeda galaxy and its Paan'uri inhabitants. Inhabitants who are intangible, interact with normal matter solely through gravity, and tend to torment other species. Y'know... kinda ghostlike.
Goblins did this in a big way. Word of God suggests that the apparent Cerebus Syndrome was intentional almost from the word go — this is supported by some bonus material in the PDF release of book one — the early farcical jokey stuff was originally written much earlier (with Kobolds), and apparently rewritten as an introduction to the story as it is today. However, it is noticeable that the comic has gotten significantly less jokey since its inception...
What was a farcical joke about how goblins inevitably receive appropriate names from the village seer became this huge plot point about the female goblin Saves-a-Fox who successfully struggled against the name given to her by killing said fox rather than saving it. It bears noting that she has saved the fox's pelt, even through being captured and held as a labor-slave by another tribe of goblins. Regarding Saves, it's revealed that the fox likely had a horrific disease and if so, she actually did "save" it by giving it a mercy killing.
The joke about how Chief was only the chief because he was named "Chief" was retconned, with Complains explaining to Chief that he only said that as a cruel joke, while Chief becoming actual leader was to avert a nasty prophecy.
Several of those early strips involved an outlandishly panicked coward very nearly dying horribly due to mishap caused by the carelessness of the other goblins, the joke being that the outlandishly panicked coward was, in fact, named "Dies Horribly". Dies went on to become a semi-regular character and was the one to make the above-spoilered reveal to Saves-a-Fox. When he does this, he is also stating and quite clearly that this joke was never a joke and that Dies Horribly ''is going to die. Horribly.He did. Then came back.
In that same vein, the spell originally used to banish Lord Incubus way back in the comic's wacky beginning (before the genesis of the title Zebra Girl, even) has a slightly less humorous feel now that it's been used on the former protagonist who is far more frightening than Lord Incubus ever was. Although, the spell still appears in the form of a magical toilet that sucks the unwanted guest in.
See also the role of henchmen in Nodwick — though their inability to permanently die is still played for laughs in the later books, there's a good deal more attention paid to why things are that way.
An early General Protection Fault arc titled "Secret Agent Geek" set the lovable slob Fooker as a James Bond knockoff secret agent, playing off as many spy-movie tropes as it could get its hands on, and finishing with a classic "It was all a dream — Or Was It a Dream?" closing. Then, years later, as the story takes a turn for the dramatic, it turns out that Fooker IS, indeed, a secret agent, possessing advanced combat skills, and access to high-tech gadgets and paramilitary troops. Nick's Inventors Gene also starts out being played for laughs, and then later turns into the catalyst for a grand plan involving seduction, time-traveling, world conquest, and The Terminator. Lampshadeed in the above quote when Trent, whose apartment Nick and Fooker had broken into to clear Trudy's name, sues Fred for libel.
Life Of Riley. What begins as a cheap throwaway joke about an artist who powers up a la DBZ when he works on computers, ends with same character resurrected as the second coming of the Messiah about to go toe-to-toe with arch-fiend Lillith over an artifact that can kill God.
Pointedly averted in Casey And Andy: despite the comic having several dramatic storylines, the strip never gives any sort of explanation, serious or otherwise, as to why the protagonists can keep coming back from the dead. Especially when other characters come right out and ask for one. (In fact, the title characters never even acknowledge any such thing has happened).
The Order of the Stick is chock full of throwaway jokes whose darker implications are fully explored later on. Some examples:
Done when Haley's greed for treasure is revealed to be so that she can pay her father's ransom money. Later subverted when it turns out she was always pretty greedy in the prequel book.
A straighter example was done with the mother of the Black Dragon from the Starmetal cave, who was mentioned lightheartedly several times during the encounter in which Vaarsuvius disintegrated her son in a scene that was still more or less played for laughs. About three hundred strips later, she appears out of the blue seeking vengeance on Vaarsuvius. This leads to one of the darkest arcs the strip has done thus far and the start of an horrific Cycle of Revenge.
Blackwing's appearance and disappearance, Played for Laughs at first in parody of D&D players' tendency to ignore the existence of familiars except for when they are needed, later becomes a serious commentary on how Vaarsuvius treats other beings, and becomes a method by which to demonstrate Character Development.
It started out as a manga-style comedy, and the protagonist was frequently subjected to the Megaton Punch, thrown out of windows, things like that. Then, once the comic went dramatic, it was revealed that he's a "Resistant" — a kind of rare, magical entity who has Nigh Invulnerability — thus making him central to the plot of an Ancient Conspiracy of mages. Upon learning that, the character comments that it's not really a major surprise, considering what he's survived in the past.
Also, his Cat Girl roommate was a normal girl that got mutated during The Weirding, turning her into a chimera and made her life a living hell.
Most of the transformations in The Wotch are played for laughs, especially those of Ming-mei and the Jerk Jocks turned cheerleaders. In the "Consequences" arc, though, Anne is horrified that she screwed up so many lives. When Ming-mei remembers being transformed, she is clearly terrified and while the cheerleaders are more or less happy as girls, the webcomic Cheer shows that Jo still is driven to tears at one point when she realizes that no-one remembers anything good about their past selves. Cassie's love potions would also fit, starting as a running gag and ending with her realizing that she had selfishly been trying to Mind Rape someone into loving her. Same with Miranda West, who first appears to be an annoying mentor, but gradually shows signs of being more sinister.
Looking for Group started with the heroic Cale'anon meeting up with Richard, a lighthearted Omnicidal Maniac, who decides to travel with the empty-headed do-gooder because it'll be fun. Except now it turns out he's on a mission to protect Cale, under orders from Cale's former master — who, right after sending him into the world, killed his wife in cold blood so he'd have nothing to come home to.
Eddie from Emergency Exit is a Cloudcuckoolander with a tendency to pull things out of nowhere. Why? Turns out it's because he FORCED A PORTAL THROUGH HIS SKULL in order to keep the villains from getting it. That's where he keeps all his random objects, and it apparently seriously messed with his mind.
A mild example in Dan And Mabs Furry Adventures: a fairly early filler strip joked about various ways the comic could get more hits, including having a character coming out of the closet and introducing a Boys Love story. Much later, it's revealed that Jyrras is not only bi, but also has a hidden crush on his best friend Dan, which he fears will ruin their friendship if ever revealed.
Jade's narcolepsy: Vriska testing her psychic powers.
Karkat's arguing with his past and future selves: an extreme sense of self-loathing which tends to manifest as him blaming himself for everything.
Gamzee's honking: becomes terrifying after the goes Ax Crazy.
Gamzee's reaction to Dave linking him to a video of Insane Clown Posse's "Miracles"? It's what pushed him over the edge and made him start killing people. Squiddles? Representations of the Horrorterrors. Finding Tavros's severed legs in a chest in Alterniabound, which prompts the narration box to ask what the hell they were doing there? Vriska waves them in his face to goad him into attacking her before she murders him. The Running Gag about Betty Crocker? She's Her Imperious Condescension, the troll Empress, and she's taken over the Alpha universe's session. Hell, this could go on all day. Homestuck is like that.
One of the earliest MegaTokyo strips has Largo being fluent in l33t as a one-off gag. Later on, l33t becomes the official third language of the series.
In the deliberately terriblePowerup Comics, many punchlines involve the Butt Monkey Dorkwinkle getting shot in the head, only for him to reappear in later strips without a scratch and without any explanation. Later, the comic gains pretensions of having an overarching story, and Dorkwinkle is explained as a genetic experiment who actually possesses the ability to recover from fatal injuries (although dying and recovering still hurts like hell).
Linkara parodies this trope in his 15 Things That Are Wrong with Identity Crisis review, saying that he got his Miller Time watch by beating up a thug in a horrifying fashion, and then buried his corpse in Nevada...then reveals that he was just giving a bad example of a Cerebus Retcon, and that his watch was just a gift.
His bouts of amorality throughout the series received this treatment at the end of his "Catwoman: Guardian of Gotham" review when after a long journey to find a famous Wizard in order to discover why his Magic Gun no longer works, the Wizard proceeds to give him a "The Reason You Suck" Speech, outlining (with clips from the show, Kickassia, and the crossovers with other reviewers) how Linkara hasn't been acting like a hero at all.
Not quite so harsh, but The Nostalgia Critic used to be proud of how he and his generation got raised by television. But as his Dark and Troubled Past became more and more clear, the pride turned bitter and "raising your kids on TV" is now one of the many things movie parents do wrong in his eyes.
On The Spoony Experiment, it's hinted that the real "experiment" at work is on Spoony himself... and he isn't even aware it's happening.
Back in season 1 of Yu Gi Oh The Abridged Series, there involves a scene where Joey is trying to "teach" Serenity how to drive. In Episode 54, however, it turns out said incident was actually the cause of Noah's "untimely death".
The "Kenny Dies" episode, where he is Killed Off for Real...not in the usual over-the-top fashion, but slowly, due to a debilitating illness, with the episode's main plot revolving around his friends trying to get embryonic stem cell research legalized in the hope that a treatment can be developed before Kenny dies. The writers eventually brought him back anyway, after which he started dying very rarely. Many of the scenes in the episode are genuinely heartfelt, although it comes to a pretty amusing thud when it's revealed that Cartman was hoarding stem cells not in an attempt to save his dying friend, but so they could clone him his own pizza parlor.
It's being played absurdly straight in the "Coon and Friends" saga. Kenny, who is revealed to be the real Mysterion, has stated that his Superpower is that he cannot die, and that even when he does die, no-one ever remembers it happening to him, (Although an earlier episode "Cartmanland" has Cartman teling people that Kenny dies all the time after Kenny dies at his amusement park. So this could be an oversight by the writers that nobody remembers him dying when clearly Cartman says otherwise) implying that he not only remembers but has experienced every death he's gone through in the series so far. One might even see it as a Deconstruction of Negative Continuity. And then there are hints throughout the episode that his ability is somehow connected to none other than Cthulhu...
In the ep "City Sushi", it's revealed Mr. Kim is an insane caucasian psychiatrist with multiple personalities that everyone just lets him be Mr. Kim by the end.
In The Venture Brothers, how Master Billy Quizboy got his mechanical hand is told through The Rashomon, and the end of the episode has him saying he doesn't really remember. A later episode shows this was because he had his mind wiped. His arm was bitten off by a pit-bull, and was given the replacement which had a monitoring device so he could act as The Mole.
Helga's family life and her bullying ways in Hey Arnold was originally played for laughs (her dad is a pompous jerk who thinks everyone should bow down to him, her mom is a scatter-brained smoothie drinker, and her sister is a Mary Sue who doesn't understand how cruel life can be, and Helga acts like a bully because she's hiding her true feelings for Arnold) — until the "Helga on the Couch" episode that reveals that she's been neglected by her parents for years and Arnold actually was nice to her on her first day of pre-school. To top it off, Craig Bartlett (the show creator) has stated in many interviews that Helga's mom is an alcoholic, but, because Nickelodeon censors didn't want alcoholism to be mentioned on the show, the "smoothies" were created as a means to let her alcoholism slip past the censors. There are also the other references to Miriam being a drunk: she once did court-ordered community service for a crime she doesn't remember doing, she falls asleep behind the couch, she had her driver's license revoked, and she tries to sober up by drinking coffee (which is actually a myth).
In the Family Guy episode "Jerome Is the New Black", Quagmire tells Brian that Cheryl Tiegs was the love of his life who left him and the break-up is the reason why Quagmire is a sex addict. Three past episodes had clues that make the revelation logical (and not just something the writers pulled out of their butts): in "Emission Impossible," Quagmire has a poster of Cheryl Tiegs on his refrigerator (during the scene where Chris shows Quagmire the objects he found on the scavenger hunt), in "The Perfect Castaway," Quagmire's reason for wanting to be blind (in a game the guys are playing) is because every woman he has sex with will, in his mind, be like Cheryl Tiegs, and in "Barely Legal" (the one where Meg becomes obsessed with Brian), Quagmire gives Meg the Shel Silverstein book The Missing Piece and tells her that he reads it whenever he feels that he needs to find the one thing in his life that's missing.
"Jerome is the New Black" also had a gag involving Quagmire's sister and her abusive boyfriend, which was played for tragic laughs (as Brian thought Quagmire's battered sister was just some one-night stand Quagmire had rough sex with). Two seasons later in "Screams of Silence: The Story of Brenda Q.", Quagmire's sister and her abusive boyfriend come back, and the abuse is Played for Drama (soul-crushing, brutally realistic, tear-jerking drama).
In the episode "Yug Ylimaf" (the 200th episode where Stewie and Brian are sent backwards through time), we see why the Greased-up Deaf Guy (a gag character who first appeared on the episode "The Thin White Line") is the way he is because he was walking beside a grease truck which suddenly exploded, burning away his clothes and leaving him soaked in grease and deafened by the explosion.
Futurama: A joke in "Where The Buggalo Roam" where Kif thought that kissing Amy (while buggalo stampeded) was making love to her was eventually fleshed out in a later episode — Kif has Bizarre Alien Biology which means that when he feels a great sense of love for someone else, his skin becomes receptive to genetic material, which is how his species reproduces. In other words, kissing Amy really was making love to her.
In a season one episode, for a bit gag, Amy's parents set her up with Kif. In the season three premiere, we learn that Kif has been hopelessly pining for Amy since then but has been too scared to ask her out again.
The first episode makes Fry's life in the year 2000 seem utterly miserable, so that it's understandable how he celebrates after being unfrozen a millennium later. Since then episodes have gone back and explored his previous life more closely, creating drama as Fry remembers his brother, beloved dog, his girlfriend, and his father.
Mutants were shown to live in the sewers in one episode, and a Running Gag developed where they would stick their heads out of the ground to yell at people. The mutants' situation is Played for Drama later, when it's revealed that Leela is a mutant, whose parents gave her up so she could pass as an alien and live on the surface.
In "Teenage Mutant Leela's Hurdles", when the cast is de-aged to teenagers, teenage Amy is shown as fat and her father makes fun of her weight. On the Comedy Central episode, "Prisoner of Benda," it's revealed that Amy was a compulsive over-eater, which is why she was fat as a kid.
Parodied in "Behind the Laughter", the outside-of-canon Animated Actors episode in which we're told that Homer became addicted to painkillers after falling down Springfield Gorge (in a well-known early episode), and that that enabled him to do "the bone-cracking physical comedy that made him a star." There is also, in the same episode, Homer feeding Lisa and Bart growth stunters via executive order in order to keep them looking the same age for the show to explain them never aging.
Most of the third season of Moral Orel does this to the first season. The first season is a comedy and Orel's life is portrayed as a Hilariously Abusive Childhood. Despite Orel's parents being pretty bad people, Orel is quite cheerful for the first two seasons, which might have made the implications of this less noticeable. It's towards the end of the second season where Orel realizes his father isn't the awesome guy he thought he was. It might be a Cerebus Retcon for Orel himself as well.