A most notable case is Gerry Conway's Parallel Lives, which while often seen as a Retcon or Revision, was actually an attempt to merge different parts of Mary Jane Waton's characterization over the Spider-Man continuity in a way that made sense, while reconciling gaps in her characterization:
Originally Lee/Romita introduced Mary Jane as an insensitive airhead who was constantly flirting and chasing after Peter in a way that was both a little insensitive and mean to Harry and Gwen, and which annoyed Peter to no end. Then Conway himself in his run building on Lee-Romita's characterization tried to develop her into a more compassionate, and courageous, person, as well as a loyal friend and companion who genuinely cares for Peter and loves him, and with whom Peter can be truly happy and relaxed in a way he couldn't with Gwen. After Conway left, Len Wein generally kept the couple as static while occasionally for the sake of drama having MJ be mean to Peter by flirting with Flash in Operation: Jealousy type gambits that left him confused, with many noting that MJ was "Gwen with sarcasm and sass" in this period, rarely building on Conway's work. Marv Wolfman, who followed Wein, had Peter propose to her and MJ reject it a little callously, seeking to end the relationship and shake the status-quo, but the second series (The Spectacular Spider-Man), still keeping in line with Conway's characterization, had her say she still loved Peter and was a little worried about taking the next step, and later Wolfman said that she did it because her parents divorced and wrote her out of the book.
When Roger Stern came and brought Mary Jane back, as a little older and more successful version of her teenage self, he also created a backstory that hinted at both her origins (with Aunt May saying that both she and Peter "have lost so much") and later an outline that as per Stern, Tom Defalco followed correctly, namely that she had known Peter was Spider-Man for a while and it was out of fear for his life and herself that she rejected his proposal and left New York. This explanation contradicted the one given by Wolfman where it was fear about her repeating her parents' divorce, and it didn't explain when she learned the secret and why she chose Peter's proposal to get out, since Spider-Man's adventures didn't impinge on her life in that period to justify her leaving.
Conway, feeling that Mary Jane's new backstory explained and deepened her early behavior and characterization, decided to have Mary Jane know from the very beginning since it both demonstrated clearly to readers how much her Lee-Romita facade was clearly an act, it heightened her courage to stay at Peter's side, made her earlier interactions and behavior with Harry and Gwen a little less mean, if still sarcastic and trollish, and provided a better motivation for her rejecting Peter's first proposal (he proposed without telling her his identity which she would obviously feel was indicative that he didn't trust her) and why she chose to reveal her Secret Secret-Keeper status to Peter and her own origins so shortly after she came back when the Puma attacked (since originally she said "I thought I could handle it before", which two issues later became a justification for her leaving New York).
The Clone Saga had one moment where Peter is arrested for deaths that were connected to the clone Kaine. To his horror, the times those people were killed were during the time he was buried alive and he has no alibi without blowing his secret identity.
The Sins Past storyline infamously Ret Cons that Gwen Stacy secretly had twins with Norman Osborn, though it doesn't try to explain how.Fandom VIP J.R. "Madgoblin" Fettinger, having pored over back issues, posted his theory online of when it could have happened: a certain period when she was on the outs with Peter but after Norman had recently saved her father's life. Maybe she went over to thank him and One Thing Led to Another? He conceded that this wasn't a perfect theory (for example, Gwen doesn't look pregnant when she logically should), but it made more sense than anything else, so the writers made it canon.note Then a later storyline reveals that this was all false anyway, she never slept with Norman and the twins were clones. Comics!
The Amazing Spider-Man (2018) tied Mary Jane's miscarriage at the end of The Clone Saga and Peter's infamous Deal with the Devil in One More Day together with the revelation that they're both part of Mephisto's efforts to prevent Peter and Mary Jane's daughter from being born, as she's apparently destined to dethrone him when he conquers Earth in a possible future.
Sinister War revealed that Kindred had been behind Mysterio's revival after the seminal Daredevil storyline Guardian Devil and was behind other events such as Spider-Men. The controversial Sins Past also plays a central role in the story, with the revelation that Harry Osborn was behind it all in a mad attempt to give Norman "worthy" heirs. That didn't pan out because the Stacy twins' bodies were too unstable, but they did come in handy when Kindred needed a body...
In Ultimate Spider-Man, several Batman Cold Opens involving him fighting some villain who attacked "Roxxon Industries" were welded together when the CEO of that company (a person rather lacking in common sense) hired some mercenaries to bring him in for questioning about why he was fighting those people.
The writers and editors of all of the Marvel Universe comics revealed that Weapon X is in fact controlled by an organization that has existed since before WWII called Weapon Plus, a secret governmental organization hellbent on eradicating mutants, who is responsible (directly or indirectly) for a LOT of the crappy stuff that Wolverine went through in his life. Also, they are (directly or indirectly) responsible for the existence of many heroes and villains of the Marvel Universe, not just Wolverine himself. They created Project Rebirth, wich makes them indirectly responsible for the creation of Captain America and Isaiah Bradley (or to be more specific, the super soldier serum, AKA Weapon I). They also created the Uplifted Animal team Brute Force and a weird squirrel with Wolverine's powers (both Weapon II), The Skinless Man (Weapon III), Man-Thing (Weapon IV), Agent Venom (Weapon V), Power Man (Weapon VI), Nuke (One of Daredevil's villains and Weapon VII), Typhoid Mary (Weapon IX), X-23, Deadpool, Huntsman (Weapon XII), Fantomex (Weapon XIII), The Stepford Cuckoos (Clones of Emma Frost and Weapon XIV), Ultimaton (Weapon XV), Allgod (Weapon XVI) and according to Word of God, they are also responsible for creating or empowering many more unknown characters, both heroes and villains. In some comics, it's also implied that they might have been involved with the program that created the Sentinels and the Red Room Black Widow Ops organization that created the multiple Black Widows (like Natasha Romanoff and Yelena Belova). The organization has also been known to work with and provide money and ressources to other villainous organizations(especially those that hate the X-men) like A.I.M., HYDRA, The Hellfire Club, ROXXON, The Purifiers, OSCORP, ect...Later on, it's revealed that Weapon Plus was created and controlled by an even GREATER greater scope villain known as Romulus. He claims to be responsible for EVERYTHING that happened in Logan's life and more, with plenty of evidence to back up said claim (Such as immense intimate knowledge of Wolverine's life, for example). The aforementioned John Sublime was pulling strings in the program as well, and to make things even more confusing, Word of God from the writer of the very first Weapon X story indicated that the original greater scope villain was going to be Apocalypse, but this never saw print for unknown reasons. Needless to say, this was revealed decades after weapon X's first appearance, wich is ironic, because Weapon Plus made its first appearance more than 75 years before it was named or written into Marvel canon, in Captain America's first appearance. Granted, Weapon Plus isn't fought often by the superheroes, but despite what anyone might believe, they are still active and plaguing the Marvel Universe with their atrocious experiments and horrifying creations...
Wolverine: In volumes 3 and 4, and in Wolverine Origins, Marvel decided to reveal Wolverine's long and complicated backstory. It turns out that just about every bad thing that ever happened to him was orchestrated by a single figure known as Romulus. This is reiterated in the handbook Wolverine: Weapon X Files, where almost every entry has a note saying "this was probably a plan by Romulus".
Kurt Busiek's Avengers Forever story indulges in arc welding throughout, revealing that every action ever taken by the villain Immortus was done in the interests of preventing the destruction of humanity by the Time Keepers. A number of seemingly unrelated plotlines turned out to have taken place under the influence of Immortus.
During his Iron Man run, Frank Tieri created a rival for Tony named Tiberius Stone. Years later, Dan Slott brought Tiberius out of Comic Book Limbo and revealed that he was the ancestor of Tyler Stone, one of the major villains from Spider-Man 2099.
In the process of doing this, it merges both versions of the New Universe, stating that the original was another form of the reimagined version.
In one of the oldest examples, Strange Tales #146 reveals that A.I.M. and the Secret Empire, previously treated as brand-new, independent threats to Nick Fury, the Hulk, and Sub-Mariner are just front organizations for a regrouped Hydra.
When Bishop first appeared in the X-Men comics, a key part of his backstory was finding a garbled tape of Jean Grey talking about a traitor in the X-Men's ranks who'd killed everyone, seemingly starting with Professor Xavier and that they shouldn't have trusted something or someone. Furthermore, an older man known as the Witness is seemingly an older Gambit, being the only survivor, which led Bishop to suspect that Gambit was the traitor. When Onslaught finally kicked off, the one-shot Onslaught: X-Men tied the tape into its plot, showing it in its entirety: Professor Xavier himself was the traitor (this isOnslaught after all), Jean believed Juggernaut was the first in Onslaught's rampage to die, that the X-Men should have suspected that Xavier's mindwipe of Magneto in Fatal Attractions (Marvel Comics) could backfire (which it did, as it's what created Onslaught), and that Onslaught didn't succeed in killing Jean when the video was cut off.
Additionally, Onslaught has his roots in the events of Fatal Attractions, as Xavier mindwiping Magneto following his ripping out Wolverine's adamantium is what led to Onslaught's existence.
X-Men: Several originally unrelated stories and characters eventually came together throughout the '90s to show that the villains Mr. Sinister and Apocalypse had been rivals since the Victorian era, and it was Sinister's attempts to create a mutant powerful enough to destroy Apocalypse for good that motivated his manipulations of Jean Grey and the Summers brothers and ultimately resulted in the birth of Nathan Summers, a.k.a. Cable. Of course, this did give rise to the famous Continuity Snarl that is Cable's backstory, which involves a post-apocalyptic future, a sibling from another post-apocalyptic future, an alien virus that turns flesh into cybernetic metal, a clone mother who launched a demonic invasion of Earth, and a crazy clone "brother."
In Classic X-Men, a random story featuring Moses Magnum where he first got his superpowers was revealed to have been the result of the machinations of Apocalypse.
Al Ewing's bread and butter is tying seemingly unrelated things together in a way that retroactively makes sense.
His run of The Ultimates (2015) ties in that series' main storyline with elements from Matt Fraction's run of Defenders, Kieron Gillen's Iron Man, and Grant Morrison's Marvel Boy. In fact, the main villain turns out to be something mentioned once in a throwaway line of the later. It also ties these elements in to something established in Ewing's work on New Avengers, the previous iterations of existence (of which the current Marvel Universe is the eighth or seventh, depending on who's asked).
Immortal Hulk ties together the Leader's plots and schemes from over the last fifty years, turning most of them into part of his plan to figure out the secrets of Comic Book Death (except turning General Ross into Red Hulk. That was partly For the Evulz). Towards the end of the series it's revealed that Gamma radiation and Cosmic Radiation are opposites, and Cosmic Rays come from the One Above All just as Gamma comes from the One Below All, who is TOAA's Hulk.
The Incredible Hulk (2023): Immortal Hulk: Time of Monsters depicts a young man in the prehistoric Fertile Crescent becoming the first Hulk when he is betrayed by his chieftain and sacrificed to a mysterious comet exuding gamma radiation. Johnson's run picks up that thread and ties it into Bruce's story; said tribal man was apparently an enemy of the Eldest and their siblings in ancient times who sealed them away in his own tomb. In the present day, an archeological team discovers that tomb and accidentally unleash the monsters contained within, and they are targeting Bruce on the basis of him being the successor to their old foe.
Meanwhile, a tie-in to Empyre for She-Hulk turns her near-death experience in the opening act of Civil War II into an actual death, as part of Immortal Hulk's exploration of Resurrective Immortality.
Marvel Comics #1000 does a truly insane amount of welding in its bridging story. To whit: (deep breath) The backstories of the Golden Age Human Torch, short-lived Timely Comics characters The Ferret and the Xs, Captain America villain Adam II, Adam Warlock and his creators, the Black Knight, several different masked heroes with the name "Raider" from Marvel's Western stories, and Guardians of the Galaxy villain Michael Korvac are tied together into one narrative. Phew. And it's hinted there are some other connections to other characters not yet revealed.
Various cosmic planes are mapped to the spheres of the Kabbalah like how the Below-Place was compared to Thaumiel in Immortal Hulk
The Beyonders were made by the Celestials to maintain the multiverse. They were also the Omega Council from a previous Defenders run, and the Concordance Engines they made created Captain Universe's Enigma Force.
Secret Wars (2015) was a 'firebreak' done in hopes of preventing the looming threat of the series.
The Tiger God is a cosmic being on the level of the Phoenix Force.
The Sentience of the Fourth Cosmos from Defenders (2021) is the Queen of Nevers.
In Infinity Wars (2018) Loki saw his past self enter the House Of Ideas. God of Stories Loki temporarily erases their memories to be the Loki of the Eighth Cosmos, who secretly had the Eternity Mask.
Ant-Man (2022) reveals that the All-Father Ultron in Ultron Forever was Pymtron from the present day after being sent forward in time and absorbing the magic holding him in the coffin from Iron Man (2020, Ongoing).
The King in Black is a role created by the Celestials, and the holder of the mantle has the job of maintaining the Multiverse like the Beyonders, albeit from another angle.
Flexo the Rubber Man, a robot from the Golden Age, was a symbiote.
The 2018 Venom series connected the titular character's mythos to both Gorr the God Butcher and Knowhere by revealing that they're all connected to the villain Knull, the Symbiote God and creator of the Klyntar race. He decapitated a Celestial whose head become Knowhere. In said head, he forged All-Black the Necrosword (actually the first Klyntar, revealing the weakness to sound and fire that symbiotes possess are the result of inherited trauma associated with the fire of the forge and sound of the hammer hitting the anvil) and was the black-clad deity that Gorr stole the sword from. The finale of the run, King in Black, reveals that Knull has an equal and opposite: The Engima Force, the power of Captain Universe.
The later Phase One films dealt with an object of power called the Tesseract and The Stinger to The Avengers (2012) revealed that Thanos was that film's Greater-Scope Villain. The Stinger of Thor: The Dark World would then tie those two together with its own MacGuffin, the Aether, when it stated that the Tesseract and the Aether are both Cinematic Universe versions of Infinity Stones, which Thanos has historically been involved with in the comics.
In a smaller instance, in the first Iron Man movie we are told that Howard and Maria Stark died in an accident when Tony was younger. Not much thought is given to this since unfortunately, car accidents are a common occurrence in real life. Then, years later during Captain America: The Winter Soldier, we find out via Freeze-Frame Bonus that the accident was deliberately caused after the Starks were targeted for assassination by HYDRA. Captain America: Civil War follows up on this by confirming that not only did HYDRA order the assassination, but Bucky was the one to carry it out, savagely beating the Starks to death.
Various, seemingly independent threats throughout Season 1, such as Project Centipede and Ian Quinn's corporation, are eventually be revealed to all be orchestrated by the same Big Bad, the Clairvoyant who turns out to be a HYDRA agent, tying into the events of Captain America: The Winter Soldier.
One of Season 2's initial main villains, "the Doctor" (Calvin Johnson, aka Cal Zabo, aka the comics Mr. Hyde) is revealed in the second half of the season to have been working on (as he perceived it) the behalf of his wife, Jiaying, who eventually serves as the season's Final Boss. She, in turn, can blame her Start of Darkness on Daniel Whitehall, the other of the first half of the season's main villains. So, in this way, most of the season's main villains were all connected to each other.
The Defenders (2017) bridges together the two different plot lines involving the Hand introduced in previous series. In Daredevil, they're established as being in a Secret War with the Chaste, while in Iron Fist (2017), they're stated to be ancient enemies of K'un L'un. Here it's revealed that the Hand was founded by exiles from K'un L'un, and the Chaste was created afterwards to serve as the Iron Fist's army to fight them in defense of the city.
Western Animation
What If…? (2021), like its comic book inspiration, is an anthology series, with each episode seemingly being a standalone affair and the only constant is narrator Uatu the Watcher. Then the otherwise-lighthearted Episode 7 has a cliffhanger with the invasion of an army of Ultron Drones, with Ultron Prime now in possession of all the Infinity Stones. The next episode sees the Watcher focusing his attention on the reality where this originated, but with the Infinity Stones, Ultron was able to sense the Watcher, and with it, learns about The Multiverse. The situation got so dire that Uatu decides to break his Alien Non-Interference Clause and calls on the heroes of the previous episodes in order to help end the threat.
