In Swamp Thing, Alan Moore famously resolved Alec Holland's quest to become human again by choosing to Take a Third Option, the Swamp Thing was never Alec Holland, the scientist was Dead All Along and his consciousness was absorbed by a swamp creature who believed he was "Alec Holland". This Downer Beginning resolved the Failure Is the Only Option nature of the premise, re-purposed and recycled supporting characters to give them new roles in a Darker and Edgier world, and Moore even allowed Alec Holland a Happy Ending reunion with his wife during Swamp Thing and Etrigan's journey to the afterlife.
Geoff Johns did this in the Green Lantern books, introducing an "emotional spectrum" that people can draw power from. The Green Lantern Corps fall square in the middle at green willpower; with red rage, orange avarice and yellow fear on one side and blue hope, indigo compassion, and violet love on the other. Not only are existing characters tied into the spectrum (villainess Star Sapphire tapping into love energy, for example), but Johns has established whole rival corps for each (like yellow ring-wielder Sinestro starting his own Sinestro Corps of fear).
It all started with his revival of Hal Jordan in Green Lantern: Rebirth. The retcon that explained away Hal's villainy also accounted for the periods of self doubt the character had been through, the graying of his hair, the reason the Spectre chose him as a host, and the reason why Hal was tempted by the power he stole while Kyle wasn't.
Before Johns, there was Steve Engelhart, who across several series and years tied together previously unrelated characters including the Jack Kirby version of Manhunter from the 1970s, the Zamarons, and the recurring mystery villain the Predator by revealing that they were all connected to the Guardians. Around the same time, Marv Wolfman showed that the Controllers from the Legion of Super-Heroes were also a Guardian offshoot.
Johns has established that the Guardians learned of the Emotional Spectrum from Volthoom, the First Lantern, and when he went mad with power, created the first seven Green Lantern rings to defeat him. Green Lanterns would reveal that the first seven Green Lanterns included a Kryptonian, a Coluan, a member of the Old Gods of the Third World, a White Martian, an ancient Tamarean, and an avatar of the Green. It also made the creator of the rings be Rami, a Guardian from the earlier Phantom Ring arc. And the Phantom Ring arc itself did it by making the main antagonist be Frank Lapinski, a minor character from Johns' Secret Origin arc.
The comic Transmetropolitan starts its Myth Arc with issue #13 (the Year of the Bastard storyline), but starts Arc Welding sometime around issue #30. Though it takes a while, events from the first issue are eventually revealed to have had an impact all the way to the last.
An early story in the first Deathstroke series revealed that a character who had appeared once in a flashback story years earlier had in fact been seeking vengeance on Slade for years and was responsible for the kidnapping and maiming of Slade's younger son Joseph and the recruitment of his older son Grant for an experiment that would kill him.
Like Moore, Grant Morrison is fond of doing this as well.
The run does this to Johnny Thunder's thunderbolt and Aquaman character Quisp, revealing they both hail from the Fifth Dimension like Superman villain Mr. Mxzytplk. Appropriately, the Thunderbolt's summoning word "Cei-U" (pronounced "say you") was revealed to be his real name "Yz" backwards and Quisp's name was modified to "Qwsp".
The finale of the run, "World War 3", also doubled as a Fully Absorbed Finale to Aztek, revealing that the "Tezcatlipoca" Aztek was trained to deal with was, in fact, Mageddon, not the Wonder Woman villain.
The Phantom Zone, the Still Zone, and Limbo are all ultimately revealed to be different names for the same place.
Pretty much everything in their run ties back to either Dr. Hurt and the Black Glove, or Talia's Leviathan organization.
It also sees Morrison tie a lot of stuff like Vandal Savage's origin and a lot of Batman's Silver Age adventures to Darkseid via the Hyper-Adaptor and its host, Simon Hurt. In keeping with them doing this in their JLA run, Bat-Mite is also revealed to be a denizen of the Fifth Dimension and the JLA run was the source of the Arc Words for this run, "Batman and Robin will never die." Also involved was the Cult of Barbatos, a demonic bat god from a 90s Batman story, and the idea that Batman subconsciously based his costume on an outfit that Thomas Wayne wore to a costume party—revealing that the Wayne family had links to the cult. Return of Bruce Wayne all but confirms that a time-displaced Batman was the source for the legend of Barbatos, meaning he may have technically inspired himself.
The Silver Age story Robin Dies at Dawn!, where Batman goes into a sensory deprivation chamber and begins hallucinating about Robin's death, among other things, proved to be a major part of these arrangements. Many strange Silver Age Batman stories, including tussles with aliens and trips to other planets, were revealed to have occurred as part of these hallucinations. One particular one, the story of the Batman of Zurr-en-Arrh, was actually an attempt to implant a hypnotic suggestion into Batman's mind that would destroy him, and the otherworldly Batman introduced in the story was a backup personality that Batman created as a countermeasure in case his mind was hit by such a suggestion.
Another Batman example: the climax of the Black Mirror arc reveals that James Gordon Jr. was involved, one way or another, in pretty much everything villainous that occurred over the course of the arc. He also implies that he was the one who inspired The Joker to cripple Barbara back in The Killing Joke, though it's unclear if that's true or if he's just screwing with her.
When DC Comics rebooted the line with the New 52 in 2011, each September issue would be part of a themed month, such as the 2012 issues being "Zero issues" exploring the revised origins of DC's heroes. Rather than derail the series, The Flash instead tied the issues into the on-going narrative.
2012: Zero issue - The debut of Daniel West, who would be revealed as the New 52's Reverse Flash over the course of the next year.
2013: Villain issues - The issue devoted to the Reverse Flash ties directly into the ongoing story arc of the time, whilst issues devoted to Grodd and the Rogues led directly into the Rogues's Forever Evil (2013) mini-series.
2014: Future's End - The issue ties directly into the Future Flash story arc that had been going on since April.
In one of the most jaw-dropping examples out there, DC Universe: Rebirth #1 revealed the true creator of the New 52 universe: Dr. Manhattan. The experiment at the end of the story gave birth to this world. Furthermore, the pre-Flashpoint and New 52 universes are the same universe.
In its first arc, Geoff Johns' run on Teen Titans does this with two of the Titans' oldest enemies, Brother Blood and Trigon. Specifically, it's revealed that the former's cult is actually a Religion of Evil built around the worship of the latter.
When John Ostrander rebooted the Suicide Squad, the backstory tied Control (of the O.S.S.) and Jeb Stuart (of the The Haunted Tank) to the original Squad, as the civilian and military heads of Task Force X. Ace Morgan also makes an appearance as a flight school rival of Rick Flag, Jr.
The Flash (2016) #761 reveals that Reverse-Flash has been using Subliminal Seduction to keep the Flash Family apart, tying together not just Rebirth-Barry constantly pushing Iris away and failing to work with the other speedsters, but Wallace going along with Damian's Well-Intentioned Extremist actions in Teen Titans (Rebirth), Bart not telling his family he's alive in Young Justice (2019) and Wally covering up the deaths in Heroes in Crisis. Speaking of that last story...
The first arc of The Flash (Infinite Frontier) revealed one: Savitar survived Eobard Thawne's attempt to kill him in the 2009 The Flash: Rebirth by escaping into the Speed Force and two: the explosion that killed the other heroes at Sanctuary was caused by Savitar in his attempt to hijack the Speed Force, meaning Wally didn't even kill anyone in the first place.
The Crisis on Infinite Earths was the first attempt, leading to the creation of the Post-Crisis Earth in an attempt to stop the Great Darkness from destroying everything, the Anti-Monitor having been corrupted into a pawn of the Great Darkness.
The handshake between the Great Darkness and the Light at the end of Saga of the Swamp Thing #50 was a truce between the two forces. However, while the Great Darkness slumbered, its influence still took hold elsewhere, leading to events like Magog's rise in Kingdom Come, Hawk becoming Extant in Zero Hour: Crisis in Time!, the Anti-Life Entity's attack in Cosmic Odyssey, Mister Mind transforming into the Hyperfly in 52, and Superboy-Prime's descent into madness in Infinite Crisis.
The Monitors' attempt to handle the new 52-Earth multiverse in Countdown to Final Crisis turned out to be an abstract failure.
Final Crisis was not one of the Great Darkness' attacks, but rather Darkseid's attempt to awaken and draw out the Great Darkness to control it for his own ends. He succeeded in awakening it, but was defeated by the DC heroes in the process and his Godhead shattered (hence why he seemed so much weaker in subsequent appearances; he restores his Godhead and full power during Infinite Frontier). Mandrakk's attack during all this was the Darkness' first direct assault, and his prompt defeat taught the Darkness that the superheroes were it's primary opponents, leading to...
The New 52 and Doomsday Clock, which were a plot by the Great Darkness to weaken the heroes by cursing Dr. Manhattan to steal time to weaken them and destabilize the multiverse.
The hand that shook the Light's hand split off to become the Empty Hand and his Gentry, the mysterious creatures from The Multiversity. Likewise, Barbatos, the bat avatar from Dark Nights: Metal, was another one of the Great Darkness' avatars and the Metal Wars another one of it's assaults.
Finally, Infinite Frontier itself and the ensuing Dark Crisis is the Darkness' next big offensive; Pariah's Face–Heel Turn is because he has become a servant of the Darkness in exchange for it reviving his family, while Deathstroke has become the primary supervillain threat on Earth as a result of a vision he received of the Darkness and it's coming (he is trying to stop it, but his methods are so extreme that he's ultimately just another threat).
Except none of the above turned out to be true. Going further into Dark Crisis, John Constantine and Swamp Thing openly bring up the first encounter with the Great Darkness and explain that it's merely the primordial darkness which existed before life began it, and it has no overt wants, needs, or desires. Furthermore, it's clarified that Pariah is the actual Big Bad, having lost his mind and suffering from hallucinations of the Great Darkness telling it what to do. Not only does it show that Pariah himself is the one using the Great Darkness, it also clarifies that none of the above mentioned events were linked to the Great Darkness at all.
The titles under the banner The New Golden Age are closely connected, and develop the reintroduction of the Justice Society and its members post-New 52 and Post-Doomsday Clock.
The one-shot has a cameo of Mime and Marionette and their biological elder son Clark, who is living in the Watchmen universe and a mysterious redhead man (Per Degaton).
The Batman (Chip Zdarsky) storyline "Joker: Year One" ties together the Batman of Zur-En-Arrh and the Joker reinventing himself as "the Clown Who Laughed at Midnight", both from Batman (Grant Morrison), with Geoff Johns' claim that there were three Jokers, which up til then had only been addressed in the non-canon Batman: Three Jokers. It turns out the Joker learned the same techniques that gave Batman his back-up personality, but embraced them more completely; there are three Jokers, and they're all him.
Live-Action TV
Arrowverse: The first episode of the second season features a group of copycat vigilantes, who among other things kill Starling City's mayor. The midseason finale reveals that they were organized by Brother Blood and Slade, in order to give Blood the opening he needs to run for mayor.
Arrow: Each season also finds a way to tie together its Present Day and Flashback storylines:
Season 1 revealed that Malcolm Merlyn was responsible for the shipwreck that stranded Oliver on the island to begin with.
Season 2's storylines are connected by Mirakuru. It was his search for it that led Dr. Ivo to the island in the flashbacks, it's being used as part of Brother Blood's plans in the present, and it's responsible for Slade's Face–Heel Turn in the flashbacks that leads to him being Big Bad in the present.
Season 3's storylines are loosely connected by the presence of Maseo, who was Oliver's ARGUS handler in Hong Kong before his son's death by the Alpha/Omega virus led to him joining the League of Assassins, becoming The Dragon to Ra's Al Ghul in the present. The final episodes tie the storylines more tightly together, however, as Ra's gets his hands on Alpha/Omega and intends to destroy Starling City with it.
Season 4's storylines also share only vague connections with each other — the organization Oliver is sent to infiltrate in the flashbacks is Shadowspire, who serve as Villain of the Week in one episode's present setting and served as part of Andy Diggle's Start of Darkness. Also, the magic idol that flashback villain Baron Reiter is after also serves as Damien Darhk's power source in the present.
Season 5's storylines have yet another vague connection in that the flashbacks have Oliver being mentored by Talia Al-Ghul, who in the present in now working with new Big Bad Prometheus.
Late in Season 3, Ra's Al Ghul reveals the existence of his rival, Damien Darhk, the leader of H.I.V.E., and that he was responsible for various episodic threats that Team Arrow had faced in Seasons 2 and 3. This on top of H.I.V.E. being responsible for Deadshot becoming a mercenary and the death of Diggle's brother.
Supergirl (2015): The episode "The House of L" ties together two of Season 4's major storylines, as Lex Luthor is revealed to have helped Ben Lockwood set up the Children of Liberty as patsies for his larger plan, and has also been helping Kaznia train the Supergirl clone known as Red Daughter.
Western Animation
Interviews with the creative team behind Justice League Unlimited and their remarks in various DVD audio commentaries reveal that they were several episodes into the production of Unlimited before they realized that they were working toward what became the "Cadmus Arc." The majority of the arc expanded upon and revolved around the events of "A Better World," an episode from season two of Justice League which had been written with no thought to an ongoing story. Cadmus turns out to have been responsible for two previously encountered (groups of) villain, Doomsday and the (Joker's) Royal Flush Gang. The ultimate reveal of the Big Bad, Brainiac, actually connected back to an episode of Superman: The Animated Series, which had been produced eight years and two TV series before the current series was even conceived. There were also throw-away lines and references that connected to as far back as "On Leather Wings", an episode of Batman: The Animated Series that was the very first entry in the DC Animated Universe, and even some Call Forwards to the chronologically-last, Batman Beyond.
