There are a lot of comic book characters or teams who have some pretty heavily convoluted histories. You'd need flow charts to track a lot of the X-Men stuff. Hawkman's history is infamous for its retcons, same with a lot of other DC characters. But if you want to to talk about a subject whose history has seen more ridiculous turns than anyone else, there's really one big contender:
The Legion of Super-Heroes
This was going to be just one post but as I was writing it, I realized it's so damn complicated so I'm going to need to break it up a bit. I'm going to keep this as tight as I can but be warned, this is going to be wild so buckle in:
The Original Era (1958-1986)
First appearing in Adventure Comics #247, the Legion was rather simple: In the 30th century, humanity has spread among the stars to various other worlds. Crime is still around, however, and when rich industrialist R.J. Brande was attacked at a spaceport, he was saved by three young teenagers: Garth Ranzz (Lightning Lad), telepath Imra Ardeen (Saturn Girl) and magnet-powered Rokk Krinn (Cosmic Boy). Inspired by tales of heroes of the 20th century, Brande got them together, funding a clubhouse (which for years was basically a rocket) and letting them be heroes. They first showed up by going back in time to Superboy and after a series of tests, granting him membership in the Legion.
Intended to be just a one-off appearance, the Legion took off with readers as Superboy would journey to the future several times, along with Supergirl. Before you ask, it was stated that Saturn Girl made sure that any details of his future (like Supergirl), Superboy would forget when he returned to his time so as not to alter history too much.
Before long, the Legion grew so popular that they started to have their own back-up stories in Superman comics. They would gain several popular members like Brainiac 5, the descendant of Superman's arch-enemy who would be a great aid, creating the flight rings members used; shape-changing Chameleon Boy; Element Lad and more. Some stories could be surprisingly adult for the time; in one, Star Boy is forced to kill an attacker in self-defense and kicked out of the Legion for breaking their no-killing vow. Another has one of Triplicate Girl's other selves killed, forcing her to become Duo Damsel. Lightning Lad seemed to die but later returned to life while Ferro Lad sacrificed himself to stop the monstrous Sun-Eater. They'd tangle with enemies like the Fatal Five, the Legion of Super-Villains, ultra-mage Mordu, Universio and the Time Trapper. A fun addition was the Legion of Substitute Heroes, made of folks whose powers aren't quite Legion material but ready to help out when needed. Much of this was written by Jim Shooter, only 14 when he started submitting stuff but built up a history that would dominate the Legion for years.
As the '70's dawned, things started to get whacky as the Legion took on trippy costumes that looked more akin to disco stuff than future super-heroes. There were also crazy stories like member Tyroc ruling a city of only black people in a story that has not aged well.
Thankfully, the '80's brought what many consider the finest creative team in the book's history, Paul Levitz and Keith Giffen. They brought a lot of cool plots like Colossal Boy seemingly hooking up with Shrinking Violet only to find it as a Durlan shapechanger but still in love with her. The high point was what is generally considered the greatest Legion story ever: "The Great Darkness Saga."
This stunning work had the Legion facing a brutal attack by servants of a dark power, pushed to the limit hard, facing the brainwashed population of Daxam who all have the powers of Superman. The duo were great working it over before revealing the foe behind it all to be Darkseid. He was defeated but gained a chilling revenge: Stealing one of the newly born twins of Lightning Lad and Saturn Girl under a wave of darkness so they never even knew the baby existed, then warping the child, sending him back in time and having him grow up to be monstrous Legion foe Validus.
Now that's evil.
DC also expanded to a brand-new Legion comic aimed at the then-new comic shop community. This was a bit darker, shown by the opening storyline of Karate Kid brutally killed, his love Princess Projecta taking revenge on his murderer and later the darker persona of Sensor Girl. It was a great time for the Legion...which was about to endure the first of many shake-ups.
Following Crisis on Infinite Earths, DC saw a lot of its history changed. A big one was John Byrne's revamp of Superman which included the fact that Clark Kent's powers grew slowly so there was no career as Superboy. This was naturally a big thing for the Legion so Byrne worked with them for a solution. First, in a mini-series, Cosmic Boy came to the new 20th century and was struck by the history different than what the Legion knew (more heroes besides Superman, space travel not as big, nuclear weapons more prevalent) and Superman not knowing him. A few other Legionnaires traveled to the 20th century to clash with Superman, who followed them to a Smallville with elderly Kents, Krypto and more Silver Age stuff. It turned out that the entire "Superboy Earth" was all a creation of the Time Trapper and every time the Legion went back in time, the Trapper shunted them to this pocket universe all as part of his massive plot to control time itself. In the end, this Superboy sacrificed himself to stop the Trapper and was honored as a hero. Byrne would return to this "pocket Earth" in his last Superman storyline as this world's version of Lex Luthor accidentally unleashed a trio of Kryptonians who wiped out all life on the planet so Superman had to execute them.
The book seemed to falter after that, having trouble adjusting to the new DC. It all culminated in a massive storyline, "The Magic Wars" where technology stops working that devastated Earth and the United Planets. Jumping ahead five years, the new book had the Legion sans costumes, more gritty outfits and waging a war against the alien Dominators that now ruled Earth. It was here that the decision was made to just remove Superboy from history altogether and replace him with Daxam hero Mon-El in some crazy time travel stuff. The era has been called way too dark by Legion fans, including a sequel to the "Great Darkness Saga" that basically ended with Darkseid committing "suicide by cape."
There were also some pretty bizarre character retcons. It was revealed Lighting Lad really had died all those years ago and it had been shape-shifting "pet" Protty posing as him all along. Element Lad had long been speculated as being gay by fans but ended up romancing science office Shvaughan Erin. However, it was now revealed Erin was born a man and had taken a drug to turn into a woman to romance Element Lad, who basically told his lover such a ruse was never necessary.
A huge turn was the discovery of a group of young clones of the original Legion, complete with powers and outfits. After some clashes, this group took on the name of Legionnaires and their own title. A storyline had Superman meeting the Legion in different time periods before a madman destroyed the moon, littering Earth with debris and rocking the Legion further.
It's damn obvious how complicated things were getting, more and more fans complaining that the backstory and history was just too much to get into. When DC came up with "Zero Hour," an event meant to clean up some of the mess of Crisis, they decided that this was the opportunity to do something long discussed: Throw out everything and start all over. In tie-in issues, the Legion and Legionnaires found themselves battling odd versions of themselves as Cosmic Boy discovered that the Time Trapper was his own future self. When some members of the Legionnaires were killed, their counterparts on the Legion also died and it turned out the Legionnaires were, in fact, the younger versions of the Legion plucked from time by the Trapper in his attempt to prevent Zero Hour from happening to no avail. The Trapper said that their history was about to be wiped out, nothing could stop it but by merging, the two Legions could find a way to keep a version alive. And so, with a massive wave of white, 35 years of history ended and a new era was to begin.
So hang on as tomorrow brings part II where things, believe it or not, get even more complicated.