I've got a question about the series that I wondered if anyone knew.
You see, I've beated the series already and went back to do it again for fun but there is one thing that kicks at me, that all the games don't explain, or I've probably passed it up. The games never said how zero disappeared in the first place, we only know that he was awaken by Ciel and that he has been gone for the past 100 years or so. But how did this awesomely powerful person go to sleep in the first place? Would anyone happen to know?

You might get answers to this question if you played Mega Man X series (particularly Mega Man X6). Somehow X7 and X8 may have messed up this logic, but not entirely sure... but I'm pretty sure X6 may answer this.

If I'm wrong, please let someone correct me since I never played the Mega Man Zero series for the fact that it was available on Hand-helds.

didnt zero die in x5 or x6 never got how he reappeared in x command mission or the other x games

As I recall, the X series was originally intended to end with X3 or X4.
So the story for the X series is all unreliable and shaky after those games.

As for why Zero is down there, I really don't know.
It was probably a weak attempt to try to connect the Zero series to the X series somehow, so I'm not too interested in figuring out what happened.

OK, I saw this thread earlier and I wanted to post then, but I didn't have enough time. Anyway here it goes. This could get complicated (I.E. most likely) so bear with me.

The Story starts with Kenji Inafune, the creator of Megaman and producer of the Onimusha series and Dead Rising for Capcom. When he started the X series of games he wanted to make the Main character Zero. However, Capcom said that Megaman wouldn't work without Megaman, so X was made the lead and Zero was put in a supporting role. Well the fans liked Zero anyway, which in turn made capcom more receptive to Zero.

With this in mind, Kenji began playing with the Megaman concept as Zero being the lead again. Kenji, who was a part of Inti creates, a company composed of ex Capcom employees that developed games for Capcom, began work on Megaman Zero. The plan was that X5 was going to be the last Megaman X game and Megaman Zero was going to start.

Now if you look at it that way and ignore the later Megaman Zero games that makes since. Zero at the end of X5 was blown apart by sigma and was only a head Torso and blaster arm. When X was gunned down and then taken away mysteriously (presumably by the spirit program of Dr. Light, Zero was left there in the remains of the Eurasia space colony which was lost to the sands of time. After a hundred Years Ceil and the resistance fighters then found the remains of the colony and in turn the remains of Zero and using her Cyber Elf Brings Zero back. being in such bad shape would have corrupted Zeros memory file which would explain his amnesia.

This sounds like it would have worked right? Well this is where it all goes south. Kenji, after X5 worked on a side project outside of capcom with the permission of Inti Creates. Well, Capcom in their infinite wisdom decided to make a sequel to X5 without Infune and Inti Creates.

Now you can't entirely fault Capcom for this move. X5 ended with the apparent death of Zero which many fans cried over. Also there was still a following for the X series. I do not know if Capcom was aware of Inafune's plan for Megaman Zero at the time but I do know that Inafune was not aware of X6's creation and plan to continue the series until after he came back and production was already underway.

So Inafune decided to alter his work slightly to try to take the X6 plot line into account. You really don't see that very much in MMZ1 because there wasn't really much need to change it. the story was vague enough not to really mess with but it did leave fans wondering (they didn't know X5 was supposed to be the last X game story wise) why zero was in such a state he was in.

Well, Megaman Zero became a hit which sparked the need for sequels. So Inafune, knowing that the discrepancies would really start to show at this point began to really rework the storyline. again not much was really altered to the storyline, however the Elf Wars are mentioned more now, the Dark elf/mother Elf seems to know Zero though if this was the original storyline Mother Elf was created after Zero went missing and could not have met, and we has our first glimpse of Dr. Weil, The main Antagonist of the series and Kenji's attempt to tie the X6 plot line to the story which unfortunately, didn't work out so well.

MMZ3 is where the storyline gets the rewrite. The next part of this will be in spoiler tags for those who haven't played the game yet. It's a fun series that should be played without being spoiled the story.

In X3 Weil is truly introduced along with Omega, the big rewrite of the story. so you play the game and it turns out that You are not the Real Zero, at least not the original body. Apparently Weil took Zero's body and used it to create Omega and ran amok during the end of the Elf War. He also corrupted the mother Elf and so on. This is the Tie in to X6 When Zero returns, apparent by repairing himself he instead created a new body or something along those lines and transferred his "soul" to the new body. Weil finds Zero's original body in the Eurasia wreckage and creates Omega with it.

So how did Zero get in such bad shape as he did if X5 isn't the way it happened? That lies in oddly enough, a soundtrack. The soundtrack for Megaman Zero 3 remastered Telos along with remastered Megaman zero 3 song includes a audio drama. (all of the zero remastered soundtracks have this) the Drama is Cyber Elf X's involvement in the story and tells Zero with his last energy his memories of Zero and what happened to him at the end of the Elf wars. It cuts to X and Zero facing up against Omega. There's some dialogue involved and then X and Zero pull a combined attack called "final Strike" which disables Omega. Afterwords it's implied that zero's body (the current one) is in bad shape and is put into a pod. Zero then tells the reploid doctor in charge to put him in stasis to study the effects of the nightmare virus within him as well as he feels that his being around is what's causing all this destruction. X rushes in too late to stop the process but they do have some final words together. Zero the sleeps for what is supposed to be a hundred years while the Virus is purged.

So yeah that was supposed to be the explanation. But, how in all likelihood most of you find my post confusing, the fans found Zero's storyline too confusing and continued to question what had happened since there was still plenty of plot holes around. Eventually, Kenji wrote off X6 from the series canon but the damage had been done because without X6, how could Zero be around during the Elf Wars, and how did Dr. Weil get his hands on Omega?

anyway, I'm done here. I hope through this mess I wrote you find some answer to your question.

SPOILER ALERT on the link below!

http://www.youtube.com/watch?v=YSih7n8T6Ls&feature=response_watch


Also here is That audio clip from the MMZ3 Telos soundtrack I was talking about. It is thankfully subbed in English so you can understand what they are talking about. Note, while the audio is officially Canon, the animation while cool as hell was created by a fan and is his interpretation of the event and not exactly canon.

Ah I see.
It has been a while since I have been able to get on but today I found some time to take a look at it.
I understand what you were saying though it took 5 read through of the explination lol.
Thanks Brimmy, I would have never imagined that this was the confusing case, I just sat one day thinking about how it started off and why, what was missing and why are some things unanswered.
It never occured to me to think of the Megaman X series because after X3, they all seemed to have been a random game put together quickly(except X5 in which I had played and actually understood) But even then, X4 and the others were just confusing. Although I was happy to see that Zero does made a comback in X6, I didn't entirely understand why, even though it was over a year ago that I last played X6.
and then I skipped X7 and watched my brother play X8, which seemed to be the worst put together game, though because zero is there, it was made better lol.
But that is all I basically have to say about that, other than the ending of Z4 was epic indeed, a well suited ending for the series.
~Silber