Once MegaMan X for SNES came out, that's when my love for the series reignited. The "lore" is what fascinated me, and for those that are clueless about the entire plot of MM here it is, with all the finer details left out:
But the finer details are what makes it so much fun! Stuff Like power sources and shit! Did you know most of the robots in Mega Man are solar powered, with the exception of Protoman, who is Nuclear Powered?
Im gonna just go all nerd on this.
Dr. Wily & Dr. Light, once colleagues, have a disagreement, causing them to become rivals.
Actually, them being colleagues is an invention by the localization team. They went to the same university, but were never colleagues professionally. Light always got the fame and admiration and accolades, while Wily, who is, make no mistake- just as much of a genius, was always the "number 2", having to live in Light's shadow.
Many many robots would soon be created by both scientists, the first being "Protoman." Through a series of conflicts Wily and his Robot Masters are continuously defeated by Light's champion, ROCKMAN!
Just because I LOVE finer details, but don't want to just repeat everything you said... ill just add to it. K?
Protoman, (also known as Blues in Japan) Built by Dr. Light, was the very first autonomous Android with humanlike thought created. (hence the name) He had a defect in his energy system however, but did not trust Dr. Light, fearing that were he repaired, he might lose his individuality. He ran away from Light, eventually collapsing from his defect. Wily came across him, and seeing the defect, decided to repair him, replacing his former Solar power reactor, with a Nuclear reactor instead. he also gave him combat capabilities, and gave him a helmet with shades, so Light would not recognize him. Protoman thus helped Wily, out of gratitude, for a while, doing his bidding. Unfortunately however, replacing his power source did not fix the defect in his energy system, thus making him unstable. Wily gave him a strong shield, so that he would have better protection from attack, since, as Protoman himself once said, "one wrong hit in the right place" could vaporize him and his immediate surroundings due to the nature of his nuclear reactor. Light, moved on, and made two more robots, Rock, and Roll, intending to keep them for himself as his surrogate children. as such, they were built in the image of such. Roll did housework, and Rock helpe him in the lab. he went on to create 6 more robots, all with industrial purposes, such as Cutman, a logging robot, and Gutsman, a construction robot, or Bombman, a demolition robot, etc.
Wily, finally deciding on a plan of action decided he would get his recognition by taking over the world. To this end, from the insight he gained of Light's robots via his repair of Protoman, he reprogrammed Light's robots to his will, and had them turn on Humanity, along with many other robots under him. Feeling a sense of duty to defeat his "brothers", Rock volunteered to stop them, and Light therefore converted him into a Combat robot, where he became known as "Rockman", (or Mega Man outside of Japan)
As time passes, both scientists' age catches up to them. After many failed attempts Wily convinces himself that he has finally created a robot that's the "strongest in the universe," one that will finally defeat MegaMan and Light, much to Bass' (his previous attempt at "1-upping MM")disbelief.
Just to add, Bass is essentially Wily's answer to Light's Mega Man. Mega Man is Light's "super fighting robot" and Bass is Wily's imitation of that idea.
Capcom till this day will neither confirm nor deny that MegaMan and MegaMan X are the same robots (there's evidence for both cases that they are different, and are the same), instead rather leave it up to the fan's imagination to come to a conclusion.
No, it has been confirmed before, (WAY back, mind you) that they are NOT the same. X is NOT Rock. They are two entirely different beings.
Light seals X away for "the world isn't ready," and Wily presumably does the same (we never actually see Zero's sealing)
Just as a tidbit- Zero was sealed away mainly because when Wily activated him, he discovered that Zero's cognitive program contained a flaw that caused him to be not only excessively violent and destructive, but to be unwilling to obey orders. SO, Wily sealed him away. The reason he never went back to correct the flaw is unknown, though it is possible he simply never got the chance.
"the ghost of Wily" (I presume it's via holographic projections from one of his many devices, same way Light communicates to X from beyond the grave)
not quite. take it as you will, but when asked about it, Inafune stated that Wily was "brought back by the Virus".
There is also overwhelming evidence to conclude that Serges from X2, and Isoc from X6, are actually housing Wily's consciousness. (Isoc therefore being the old man Sigma mentions in X5)
and tells him that the Virus purifies Zero and he must be reunited with it, to fulfill his destiny of defeated MegaMan X and thus gaining ultimate victory over Dr. Light. Zero becomes momentarilly infected but his good will refuses, thus thwarting Wily's plan and X defeats Sigma. However, the Maverick Wars continue.
Actually, Zero has always been infected. I assume you mean the fight between X and Zero, although the actual scenario as followed by the timeline, is of Zero NOT going Maverick. However, Zero has always been a carrier and spreader of the Virus himself. Him and Sigma were infected at the same time during their fight, from Zero's capsule, which had actually been the containment source for the Virus.
Dr. Weil steals Zero's body
he actually obtained it perfectly legally. He asked the Government to use the body, since it was immune to the Virus, and they gave it to him. it was once he created Omega that he turned on the government and unleashed Omega upon all who opposed him.
the other scientist created a duplicate body for him to occupy.
probably semantics, but we dont know the circumstances surrounding Zero's copy body. We don't know who exactly made it. It was not the same person who created Cyber Elves.
The humans of earth have a trial for Dr. Weil and punish him by putting him in a cyborg body, so he will never die, and "eternal punishment." The year is now 22XX.
Just to elaborate, they illegally punish him WITHOUT a trial. He was essentially attacked by a lynch mob of survivors of the war, who after giving him an immortal regenerative body, exile him into the wastelands his war created. By then, there is really only ONE last remaining bastion for Humanity, the rest of the earth is a wasteland. He is cast out into this, so as to experience eternal death. Always dying, but never being able to fully die and end his suffering.
Ciel, descendant of the original scientist that created the Mother Elf, awakens Zero to help her stop Copy-X, a deformed copy of the original X that has gone rogue.
Again, just for clarity, when X sealed Dark Elf within his body, his soul was pushed out and split into 5, 4 of which were used to create Copy X's 4 guardians, (classified as "X-Bioroids") and Copy X, was initially intended to be a replacement body for X himself, but he refused to come back, and thus they instead turned the shell into a copy to replace him, so that the people would not despair that their savior (and then ruler) was no longer. His going rogue, was essentially caused by a naivete, lack of experience, and massive ego. Not to mention a massive chip on his shoulder. he decides that to solve the energy crisis and keep Humans happy, he will start to indiscriminately execute Reploids, since they are big energy users, thus creating an oppressive regime against them.
He builds a giant space station, named "Ragnarok," that would obliterate literally everything on the planet.
just a note on the space station and all that, one of the main plot points of Zero 4, is that Nature has once again started to grow outside of Neo Arcadia, the previously mentioned "last remaining utopia". When the space colony from X5 crashed, it's environmental system survived and began to cultivate nature all around the area. So Weil, naturally, wants to destroy it so all must live under his reign.
Several hundred years pass,
semantics, but 200 years, to be exact.
(humans trading their bodies for Reploid bodies, and vice-versa)
to clarify, Humans gain robotic cyborg bodies, while Reploids gain lifespans.
Thousands of years later, a "blue boy" is discovered by Barrel & Roll Casket.
Barrel is the one who discovers him. On one of his adventures in forbidden, (and un-enterable) ruins, he discovers a baby within a stasis field, accompanied by a robotic monkey (just roll with it) he raises the kid, along with his granddaughter Roll, after her parents disappear in an accident.
They go on various adventures to find energy,
to clarify, this future world is mostly water, with small islands housing towns. the energy source is provided by crystals, which are obtained from ancient ruins and the like, thus establishing ruin hunting as a profitable business. (which Barrel used to do when he was young, and that which the boy he found, he has raised to do) f
To be continued when I get home...
Ill continue!

The boy is named Rock. (Mega Man in the US translations) he is essentially a kind of cyborg. to elaborate, although technology seems to have regressed to pseudo-21'st century, (aside from things like massive airships and the power source, most things seem very modern day commonplace) technology regarding the body still seems advanced, as it is possible to become a cybor and replace your body parts. ruin hunters, (called Diggers) often do this, to better aid them. Barrel himself has robotic eyes and ears, and Rock, also has an entirely cybernetic body, which he can interchange with a blue armor he uses while Digging. with this armor equipped, he can replace parts such as his arm, with weapons and tools. Roll meanwhile, acts as his navigator, using radar and such to guide him through ruins that are often found deep under most islands and the outskirts of towns. The robot monkey meanwhile, (called Data) acts, gameplaywise, as a save point. strangely, Rock is the only one capable of understanding what the robot says.
Within these ruins are rogue robots called "reaverbots", which attack all intruders, but which have no basis in society, seeming to be leftovers from whatever civilization previously lived on the planet. Eventually, Rock and Roll make their way to the center of some complex ruins, to discover and accidentally open a capsule containing what appears to be a pleasant man with purple hair and a primitively robotic floating body and limbs. This person, (called Juno) recognizes Rock, and identifies him as "Mega Man Trigger", a "Purifier Unit, first class), and proceeds to thank him for awakening him, and reveals that it is his duty to monitor the population of the island, the people, whom he refers to as "Carbons", and prevent them from reproducing beyond a certain limit. Once they do, it is his job to "purge" the Island, killing all on it. This job continues every time the population exceeds a certain limit. Eventually, Rock catches up to Juno deep within the ruins, where they do battle. All the while, far up in space, a probe is released from an abandoned satellite and descends over the town, prepared to purge it. Once Juno is defeated and destroyed, Data steps in, and commands the "system" to interrupt the command given by Juno, and declares that under suspicion of malfunction, Juno was terminated, and Rock will assume Juno's duties until he petitions for guidance later. The probe retracts, and acknowledges the command. Data tells Rock that he cannot tell him anything yet, but will do so in due time.
The next adventure revolves around Barret and his former digger partner, setting up an expedition to the mysterious siland on which Rock was found. It is protected by severe weather, but Rock manages to penetrate, and after defeating more reaverbots, discovers a stasis field with two strange people in it. They have dark skin, green hair, and wear strange clothes. They are taken back to the ship, where the people on board, Barrel and his friend included, decide they must be Ancients, the previous inhabitors of the world and the people the ruins are left from.
Long story short, they are not actually ancients, but part of the same system as Juno, and try to do the same thing, that is, "purge the carbons". this time however, Rock learns more about his past. he himself was part of that ancient system, as a "purifier unit", a unit that hunted down and terminated rogue machines and other units. (sort of like the Maverick Hunters of the Mega Man X series)
Humanity had left the earth, and established a paradise on the artificial moon called "Elysium". they did not die, they did not need, and they had no wants. it was utopia. They had various robots as well, who maintained the system and the planet. Juno, like Rock, and the two"Ancients" are of these robots. However, all the Humans eventually died out, And "The Master" a Human who had lived thousands of years, and was the creator of the system, decided that they System itself had crown too cold and sterile, and that Humanity had lost essentially, their Humanity. The population of the planet, "Carbons" were artificial Humans created by the people on Elysium. The Master decided that they were truly Human, and asked Rock, Mega Man Trigger, to take him there. He cannot survive outside of Elysium, but before dying, he orders Rock to destroy the system in it's entirety, and gives him his genetic sample, since, once the last Human had died, the world would be purged of all Carbons and Humans would be re-cloned from a massive genetic library. Having The Master's genetic code would therefore make him harder to attack, since it would mean risking the genetic Code. Hoe does however, eventually fight to a standstill, with one of those two ancients they had found, named Sera, who was the unit in charge of the systems on Elysium, damaging both severely. Trigger to survive, downloads his memory (and the genetic sample) into Data, the robot monkey, and resets his body to regenerate, thus resetting his body to that of an infant. The unit that had been in charge of the planet's systems, (She was named Yuna) and had declared herself neutral. She seals both away, until Barrel eventually found the boy and raised him.
Sera after showing her true colors, returns to Elysium and plans to finish what went undone since their final battle, and Rock follows. They fight and Sera is defeated, though not killed- although she learns of Rock's intentions and the Master's dying wish, finally understanding it and seeing Rock's point of view. However, Rock, Sera, and Yuna, are left stranded on Elysium with no means of escape. back on the planet, Roll vows to get him back, and her and Tron, one of the pirates that you fight multiple times across the two games- who had grown infatuated with Rock, try time and time again, to build a rocket to Elysium. When i mentioned technology had regressed, I should have mentioned, there is no space travel either.
And thats really where the Mega Man timeline ends, since the third Legends game was cancelled.
As you can see, yes, I love the lore. Im a big sci fi guy, and the idea of robots and such always fascinated me. I just liked how it was presented by Capcom, and Mega Man has been present in my entertainment since i was very little,