Capcom doesnt consider X7 and X8 canon. The story ends in X6 when Zero goes to "Sleep" at the end of the and picks up with Zero 1. They were made purely out of sales and should not be considered part of the offical storyline.
Capcom released a booklet of the ENTIRE plot line of the Mega Man plotline and someone translated it at the ign boards. It will answer every damn question you can think of:
In case you haven't heard of it, it was released a couple of years ago in Japan as part of the Megaman 15th anniversary. It's basically an encyclopedia of sorts on the entire Megaman series (Megaman -> Megaman X -> Megaman Zero -> Megaman Legends), and explains quite a bit about the relations of the series. Back in High School, I had a friend who was able to loosely translate the sourcebook, and explained to me the connections between the series. I've lost touch with him since we graduated, but I still remember most of what he said. An official translation does not exist to my knowledge, so I just had to take his word for it. While about 70% of the information here is straight from the book and the events in the games, the other 30% can be determined by logic and obvious connections. Here goes:
Megaman was originally created as a robot to help humans by Dr. Thomas Light. Light's assistant at the time, Dr. Wily, became jealous of his creations and vowed to make his own creations superior to Dr. Light's. Thus Wily began to destroy other creations by Dr. Light by converting some of their original robots into war machines. Megaman requested that Dr. Light modify him into a war machine as well in order to combat the actions of Dr. Wily.
Several years and mounds of destroyed robots later, Wily created Zero as a last ditch effort to defeat Mega Man after Bass had failed to do so. In Megaman 8, something called "Evil Energy" fell to earth with a robot named Duo who had been sent to destroy it. Wily kept some of this evil energy and later used it combined with the original plans of Bass to create Zero. Because all of Wily's other attempts had failed, he decided to sacrifice the ability to control Zero in order for all the output energy to be focused into power. In other words, Zero had the ability to think and make his own decisions, therefore he was the first Reploid.
However, this evil energy used to create Zero was able to possess him, and he went maverick. Zero ends up killing Wily, Bass, and wounds Megaman in a fight. Zero at this point vanishes (the book isn't really clear on what happens to him, or what he does during this time). Light decides to rebuild Megaman similar to Zero, except equipped with an anti-virus to the Zero virus (the evil energy that lies within Zero) instead of the evil energy. However, because the anti-virus has similar properties to evil energy, Light decides to run a several-year test on Megaman to ensure that he wouldn't go maverick as a result. (he said that it's hard to tell if the book said Megaman X was "of the same" or "is the same" as the original Megaman, but it is speculated that X is indeed the same model as the original).
That's where Dr. Cain finds Megaman, renamed Megaman X, much later. Cain uses the data from X to recreate other reploids like him. However, some of the reploids become mavericks (most likely because they weren't subject to the long-term diagnostic that X was). Cain then created Sigma as a result. Sigma gets a report of an unusual energy signal, and goes to investigate it (this is the cut scene in X4 of the fight between Zero and Sigma). During this fight, the evil energy is transferred partially to Sigma as a result of him shattering Zero's energy core. This creates the Sigma Virus. Zero's body is not destroyed, and he is reactivated by Dr. Cain. The evil energy within him becomes dormant at this point. Then Sigma goes Maverick, and all the events between X and X6 transpire. The nightmare is another term for Zero's evil energy. Also note that in X5, X mentions building a haven for humans and reploids called Elysium (this location is visited in Megaman Legends 2, and is explained later on).
According to Perfect Memories, the canonical ending to X6 is the one where Zero enters a chamber Dr. Light built for 100 years in order to erase the Nightmare from his system. (Inafune, the creator of Megaman, intended to conclude the X series with X6, however sales in Japan and the chance to do a MMX game for the PS2 persuaded him into making X7, and eventually X8 and Command Mission. If looking at Megaman X from a standpoint of all the series, X7, X8, and Command Mission are just side stories and are not part of the main arc) Zero is revived by Ciel about a century later, and that's where the Mega Man Zero series starts. Zero battles on the side of the humans, and learns that X has disappeared, but his DNA has copied into several other reploids. At the end of the first Megaman Zero, we learn that X is resting and wants Zero to battle the nightmare for a while longer.
This is because X is using Zero as a distraction. X has built Elysium, and several human survivors and reploids live there. X eventually has his program removed from his body and installed in Elysium's main computer. The anti-virus in X's body acts to shield Elysium from the Zero Nightmare, and the humans and reploids continued to research ways to destroy the Nightmare.
Eventually (although we can't determine exactly when because the Zero series is currently on hiatus and may not be completed like Inafune planned), the citizens of Elysium discovered a way the Zero Nightmare could be stopped. X's program was removed from the mainframe of Elysium's core, and his DNA was infused with artificially-created water. Using this, Elysium flooded the planet with the anti-virus data and finally wiped out the Zero Nightmare. Because X was gone and no longer able to guard the system, the "Mother" unit Sera was created to guard Elysium and its inhabitants. Several other units called "reaverbots" were also created to guard the Master system from harm. (it is unknown what happens to Zero, but it is assumed that he finally dies for good)
The remaining humans wished to repopulate the planet (which is now known as "Terra") by using human data in Elysium's Core. Unfortunately, this is interpreted as a threat to the master system by the Reaverbots. Sera is not able to stop the reaverbots as they are protecting the master system and attacking them would go against her coding, likewise, she does not attack the humans as that goes against her coding as well. The reaverbots are able to kill all but one of the humans, who was able to shut down the reaverbots by restarting the core. This human is the "Master" that we see in Megaman Legends 2. The only inhabitants of Elysium at this point are Sera and the Master. The Master reconfigures Elysium's core so the creation of humans is not seen as a threat, and begins recreating humans on Terra. These humans are called "carbons", as they are not truly human. The Master then creates a model identical to Sera, called Yuna, to guard the humans and Terra in case the reaverbots on Terra try to attack them. Yuna is able to confine the reaverbots inside old ruins from the Megaman Zero series, and the carbons are able to live a normal life. As a failsafe, the master sends Megaman Juno to guard the ruins so the carbons won't reactivate them.
However, the Master becomes old, and with the carbons on Terra evolving, he decides to destroy the core of Elysium, and let the carbons live on their own without the Core system to interfere. However, the Master can't destroy the core system itself because a part of X's DNA is what created it, and that same data is needed to shut it down. To solve this problem and destroy Elysium's core, the Master creates Megaman Trigger, a near-perfect copy of X, using a part of X's DNA. Because Trigger has X's DNA in him, he possesses the ability to override the core and destroy it. Sera however, recognizes this as a threat to Elysium's core, which she was created to protect. Sera and Trigger have an intense battle on Terra, which eventually comes to a standstill.
Yuna, who is still the guardian of Terra, sees both of them as a threat to the carbons and to Terra itself. She also assumes that Trigger's command to wipe out Elysium's core is an error in his programming and was unintentional. Taking advantage of their fatigue from battling each other, Yuna freezes both Sera and Trigger in stasis diamonds, wipes Trigger's memory, and then hides them both inside the ruins. A few decades later, Trigger is found by Barrell and that's where the Legends series starts.
Whew...that about does it.
Capcom released a booklet of the ENTIRE plot line of the Mega Man plotline and someone translated it at the ign boards. It will answer every damn question you can think of:
In case you haven't heard of it, it was released a couple of years ago in Japan as part of the Megaman 15th anniversary. It's basically an encyclopedia of sorts on the entire Megaman series (Megaman -> Megaman X -> Megaman Zero -> Megaman Legends), and explains quite a bit about the relations of the series. Back in High School, I had a friend who was able to loosely translate the sourcebook, and explained to me the connections between the series. I've lost touch with him since we graduated, but I still remember most of what he said. An official translation does not exist to my knowledge, so I just had to take his word for it. While about 70% of the information here is straight from the book and the events in the games, the other 30% can be determined by logic and obvious connections. Here goes:
Megaman was originally created as a robot to help humans by Dr. Thomas Light. Light's assistant at the time, Dr. Wily, became jealous of his creations and vowed to make his own creations superior to Dr. Light's. Thus Wily began to destroy other creations by Dr. Light by converting some of their original robots into war machines. Megaman requested that Dr. Light modify him into a war machine as well in order to combat the actions of Dr. Wily.
Several years and mounds of destroyed robots later, Wily created Zero as a last ditch effort to defeat Mega Man after Bass had failed to do so. In Megaman 8, something called "Evil Energy" fell to earth with a robot named Duo who had been sent to destroy it. Wily kept some of this evil energy and later used it combined with the original plans of Bass to create Zero. Because all of Wily's other attempts had failed, he decided to sacrifice the ability to control Zero in order for all the output energy to be focused into power. In other words, Zero had the ability to think and make his own decisions, therefore he was the first Reploid.
However, this evil energy used to create Zero was able to possess him, and he went maverick. Zero ends up killing Wily, Bass, and wounds Megaman in a fight. Zero at this point vanishes (the book isn't really clear on what happens to him, or what he does during this time). Light decides to rebuild Megaman similar to Zero, except equipped with an anti-virus to the Zero virus (the evil energy that lies within Zero) instead of the evil energy. However, because the anti-virus has similar properties to evil energy, Light decides to run a several-year test on Megaman to ensure that he wouldn't go maverick as a result. (he said that it's hard to tell if the book said Megaman X was "of the same" or "is the same" as the original Megaman, but it is speculated that X is indeed the same model as the original).
That's where Dr. Cain finds Megaman, renamed Megaman X, much later. Cain uses the data from X to recreate other reploids like him. However, some of the reploids become mavericks (most likely because they weren't subject to the long-term diagnostic that X was). Cain then created Sigma as a result. Sigma gets a report of an unusual energy signal, and goes to investigate it (this is the cut scene in X4 of the fight between Zero and Sigma). During this fight, the evil energy is transferred partially to Sigma as a result of him shattering Zero's energy core. This creates the Sigma Virus. Zero's body is not destroyed, and he is reactivated by Dr. Cain. The evil energy within him becomes dormant at this point. Then Sigma goes Maverick, and all the events between X and X6 transpire. The nightmare is another term for Zero's evil energy. Also note that in X5, X mentions building a haven for humans and reploids called Elysium (this location is visited in Megaman Legends 2, and is explained later on).
According to Perfect Memories, the canonical ending to X6 is the one where Zero enters a chamber Dr. Light built for 100 years in order to erase the Nightmare from his system. (Inafune, the creator of Megaman, intended to conclude the X series with X6, however sales in Japan and the chance to do a MMX game for the PS2 persuaded him into making X7, and eventually X8 and Command Mission. If looking at Megaman X from a standpoint of all the series, X7, X8, and Command Mission are just side stories and are not part of the main arc) Zero is revived by Ciel about a century later, and that's where the Mega Man Zero series starts. Zero battles on the side of the humans, and learns that X has disappeared, but his DNA has copied into several other reploids. At the end of the first Megaman Zero, we learn that X is resting and wants Zero to battle the nightmare for a while longer.
This is because X is using Zero as a distraction. X has built Elysium, and several human survivors and reploids live there. X eventually has his program removed from his body and installed in Elysium's main computer. The anti-virus in X's body acts to shield Elysium from the Zero Nightmare, and the humans and reploids continued to research ways to destroy the Nightmare.
Eventually (although we can't determine exactly when because the Zero series is currently on hiatus and may not be completed like Inafune planned), the citizens of Elysium discovered a way the Zero Nightmare could be stopped. X's program was removed from the mainframe of Elysium's core, and his DNA was infused with artificially-created water. Using this, Elysium flooded the planet with the anti-virus data and finally wiped out the Zero Nightmare. Because X was gone and no longer able to guard the system, the "Mother" unit Sera was created to guard Elysium and its inhabitants. Several other units called "reaverbots" were also created to guard the Master system from harm. (it is unknown what happens to Zero, but it is assumed that he finally dies for good)
The remaining humans wished to repopulate the planet (which is now known as "Terra") by using human data in Elysium's Core. Unfortunately, this is interpreted as a threat to the master system by the Reaverbots. Sera is not able to stop the reaverbots as they are protecting the master system and attacking them would go against her coding, likewise, she does not attack the humans as that goes against her coding as well. The reaverbots are able to kill all but one of the humans, who was able to shut down the reaverbots by restarting the core. This human is the "Master" that we see in Megaman Legends 2. The only inhabitants of Elysium at this point are Sera and the Master. The Master reconfigures Elysium's core so the creation of humans is not seen as a threat, and begins recreating humans on Terra. These humans are called "carbons", as they are not truly human. The Master then creates a model identical to Sera, called Yuna, to guard the humans and Terra in case the reaverbots on Terra try to attack them. Yuna is able to confine the reaverbots inside old ruins from the Megaman Zero series, and the carbons are able to live a normal life. As a failsafe, the master sends Megaman Juno to guard the ruins so the carbons won't reactivate them.
However, the Master becomes old, and with the carbons on Terra evolving, he decides to destroy the core of Elysium, and let the carbons live on their own without the Core system to interfere. However, the Master can't destroy the core system itself because a part of X's DNA is what created it, and that same data is needed to shut it down. To solve this problem and destroy Elysium's core, the Master creates Megaman Trigger, a near-perfect copy of X, using a part of X's DNA. Because Trigger has X's DNA in him, he possesses the ability to override the core and destroy it. Sera however, recognizes this as a threat to Elysium's core, which she was created to protect. Sera and Trigger have an intense battle on Terra, which eventually comes to a standstill.
Yuna, who is still the guardian of Terra, sees both of them as a threat to the carbons and to Terra itself. She also assumes that Trigger's command to wipe out Elysium's core is an error in his programming and was unintentional. Taking advantage of their fatigue from battling each other, Yuna freezes both Sera and Trigger in stasis diamonds, wipes Trigger's memory, and then hides them both inside the ruins. A few decades later, Trigger is found by Barrell and that's where the Legends series starts.
Whew...that about does it.
)
Revisionist history, at best(still a big freaking stretch).
