You know how Jughead from Archie Comics wears that crown hat thingy? In The '40s when the comic began it was an actual trend to cut up fedoras; decades later this is forgotten and Jughead wears a funny hat because he's Jughead. Archie Comics (2015) on the other hand has him as the son of a wealthy family who was swindled out of everything and became poor. He cut up the hat he once wore as a sign of being all high-society.
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.
In "The Thief and the Billionaire" it's revealed that, after his falling out with his sisters, Scrooge had come back to Duckburg at least twice to try and reconcile, only missing them because they were out of town. And the second time Fantomius' threat to steal everything he had as soon as it wasn't under Matilda and Hortense' care anymore prompted him to stay away until 1930, preventing their reconciliation.
In The Life and Times of Scrooge McDuck it's shown that Scrooge received a hero's welcome when he returned to Duckburg for good in 1930, only for him to take the ceremonial keys of the city and break them on the mayor's head. In the "The End and the Beginning" five parter it's revealed that Flintheart Glomgold had taken advantage of Fantomius being stranded in time to take credit for his defeat and get elected mayor of Duckburg, robbing the citizenship blind until Fantomius returned, retrieved and redistributed most of the money, and chased Glomgold out of town, with the vice mayor becoming full mayor, shortly before Scrooge's return — and all of that had happened during The Great Depression. Scrooge's return was seen as the start of Duckburg's economic recovery after all of that, hence the welcome... And while that's what would happen, he also traumatized everyone by giving the impression of being another Glomgold, only richer.
The first issue of the official Invader Zim continuation comic does this in regards to Zim's relationship with his Friend in the Black Market/Knowledge Broker, Prisoner 777. On the show, 777 seemed to be helping Zim purely for the hell of it (or, with some Alternative Character Interpretation, as a way of messing with the Irkens), but the comic reveals that Zim is actually holding 777's kids hostage in exchange for his services. Though, given this franchise's tone, even this twist is Played for Laughs: the kids seem cheerfully oblivious to the danger that they're in and 777 seems more exasperated than scared about Zim's threats.
Gilbert Hernandez's Love and Rockets and related work: Dios mio, poor Fritz. Initially introduced as a sexy, funny, kinky, Really Gets AroundCloudcuckoolander, once she starts getting stories centering around her it becomes increasingly obvious that she's an incredibly damaged but heartbreakingly, unjustifiedly, optimistic woman who's been sexually and financially exploited and emotionally abused by just about everyone she's ever known except her sisters.
Jaime's half of the series also featured at least one major retcon of this type. Early stories of the Hoppers 13 (a.k.a. Locas) books were slightly campy, pulpy affairs, lending the "Rockets" to the "Love & Rockets" title of the larger comic. These stories had Maggie interacting with aliens, dinosaurs, robots, rocketships, interplanetary travel, and hovercars, all occupying a fictional retrofuturist setting. Later stories eliminated the science fiction elements completely and shifted the settings to the real world. Later comics retconned the early stories by saying that Maggie's memories of that period had become muddled by LSD use and too many 1950's sci-fi comic books.
Miracleman by Alan Moore served as a grittier take on the Marvelman comics by L. Miller & Son Ltd. (the name being changed to "Miracleman" when Marvel Comics threatened litigation), part of the premise being that Micky Moran, Dicky Dauntless and Johnny Bates' abilities to transform into their respective alter egos Miracleman, Young Miracleman and Kid Miracleman, initially believed to come from an astrophysicist who discovered the key harmonic of the universe granting Micky these powers and Micky subsequently giving Dicky and Johnny powers of their own, were actually the result of a secret government experiment intended to make them into living weapons, their whimsical adventures in the original comics of the 1950s and 1960s retconned as being a simulation that the lads had been kept inside before they were needed. The Miracleman Family's final mission ended with the backers of the project attempting to kill them after slowly realizing how dangerous they'd be, with Moran and Bates surviving (the former living a normal life before remembering that he can become Miracleman by saying "Kimota" and the latter coasting through life by staying in his Kid Miracleman form at the cost of becoming a depraved psychopath).
At the end of her arc in My Little Pony: Friendship Is Magic (IDW), Chrysalis and her Changelings got a humorous defeat when her castle partially crumbled around them, trapping them inside with nobody except themselves and a magically animated costume of Pinkie Pie for company. In her issue of Fiendship is Magic, it's revealed that Celestia has rebuilt the ruins into a fully-functional prison, complete with magical barriers, anti-exfiltration scans and a dedicate troop of guards. Oh, and they're going to stay in there for at least a thousand years before being considered for parole. And Chrysalis has had a Villainous Breakdown due to learning about Twilight ascending to Alicorndom, scribbling insanely all over the castle as a result.
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 genuinely pathetic, dangerous and destructive he used to be. 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.
The retool of Rat Queens came back with more jokes and short conflicts. The next arc reveals that a one-off was the new Big Bad probing the team for psychological weaknesses.
In the final Scott Pilgrim book, Scott learns from Kim that the very quirky flashback of book 2 wasn't very quirky at all. He ended up with Kim after some sort of altercation with a guy Kim was dating, Simon Lee (the circumstances aren't known, but Kim mentioned hugging and it's implied it was Poor Communication Kills). Furthermore, he told his best friend Lisa Miller that he was moving to Toronto and asked her to tell Kim instead of him doing it himself, which led to Kim and Lisa not talking for a month. Though the incident with Simon was mentioned beforehand (Kim called Simon a jerk and called Scott one too, though half-heartedly with the latter). She later admitted it was partially her own fault for her reaction. Also, Scott's memory problems revealed to be the result of Gideon tampering his memories For the Evulz.
Antoine D'Coolette, the easily scaring comic relief of the group who Sonic loves to make fun of is discussed by Bunnie in Issue 46 of Sonic the Hedgehog (Archie Comics). Turns out he was once much more valiant and composed way before Sonic joined the Freedom Fighters, and clever enough to save Bunnie's life on one occasion. He lost his way after his father was roboticized, wearing his father's uniform and attempting desperately to win Sally's love for the purpose of filling the emotional void his loss left him.
Street Fighter: 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. Go is brutally beaten to death by Sagat and Dan is left traumatized. Then, in a much later series, a now remorseful Sagat actually offers to let Dan kill him as penance.
In most versions of Teenage Mutant Ninja Turtles, the Turtles' famous color-coded ninja headbands are one of the most unabashedly goofy elements of the Turtles' design. Even when the franchise is at its Darkest and Edgiest, there's something inherently silly about seeing four giant turtles walking around a crowded city wearing nothing but tiny cloth scarves around their heads. But the IDW comic book series explores the idea that the Turtles weren't just randomly mutated by ooze, but are actually reincarnations of Hamato Yoshi's four biological children who were murdered by Oroku Saki. When they were alive, Yoshi's sons always wore red, blue, purple and orange, respectively; as the Turtles, they still wear those colors as a marker of their previous lives, even if they don't understand why.
The Utroms are a race of brain-like aliens found in multiple ninja turtle series that prefer to travel in the chests of humanoid mech-suits but the IDW series gives a dark explanation as to why. They originally evolved as a race of intelligent Puppeteer Parasites who used this ability to become the dominant species of their homeworld and their faces would be visible on the chests of their hosts, their tendency to use suits designed like that is likely a forgotten instinct.
The original G1 cartoon had a number of characters who in addition to being giant transforming robots also had special powers just because. It's revealed that in Pre-war society these individuals were subject to discrimination becuase their abilities made them difficult to classify.
Many G1 Autobot leaders, like Hot Spot, Thunderclash, and Star Saber, were characterized as clones of Optimus Prime. Brave, selfless, devoted moral paragons derivative of the original supreme commander. The Transformers: Last Stand of the Wreckers suggests that these characters were suffering from mental illness manifesting as hero worship causing them to suppress their own personalities and alter their bodies to better resemble the object of their obsession.
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.
