I'm really happy with how everyone has responded to this story but now, reading it about two years after it was published, I fell like something's missing.
And I know what that is now.
I found out about Axl, now I have a theory for why he didn't appear or was never mentioned in Megaman Zero, the first game in the Megaman Zero series was released in 2002, while the first game with Axl in it was released in 2003, a whole year after Megaman Zero.
Axl could have still been in development when this happened, so the creators of Megaman Zero didn't know about him, which meant that they couldn't put him in the game.
And while some people could argue that Axl could have been mentioned in the other Zero games but I think that by that time, they already had the story planned out and there wasn't a place for him, which leads to my three favourite theories for why he didn't appear.
1) Axl died during the Elf Wars.
2) He was sealed away like Zero and nobody has found him, anyone that knew about him could be dead by the time of the Megaman zero series which means that his location and Axl himself has been lost forever, unless someone finds him, because in the ending of X8, it is implied that Axl was inflected with a virus and we don't know what virus it is. Zero was sealed away to be cured of the Maverick Virus so it is possible that the same thing happened to Axl.
3) This one is my favourite one and my personal one, I don't know if anyone else has thought about it but this is my explanation for Axl not appearing in the Megaman Zero series.
My theory is that the Megaman Zero series and the last two games in the Megaman X series (X7 and X8) take place in two different timelines, because if you watch the endings of X6, you can see that there is a difference between the two endings, and it is Zero.
In the first ending, both X and Zero appear, standing side by side, while in the second one, it's just X and Zero is being sealed away in a capsule in another location.
This is where the timeline for the Megaman X series splits, the first ending leads to the timeline where X and Zero met Axl while the second ending leads to the Megaman Zero series.
And people can argue that the Megaman Zero series can happen in both timelines which still leaves the question of why Axl wasn't mentioned or appeared in the Megaman Zero series, which leads back to my other two favourite theories, he died in the Elf Wars or he was sealed away.
And just like X and Zero, I don't own Axl but if I did, he would get his happy ending as well.
You idiots.
You stupid stupid idiots!
X, Zero, you're idiots, really stupid idiots...
Why?
Why did it have to be you two?
Why did the world and everyone in it have to be so selfish?
Even me...
I should have said something, I should have done something...
But I didn't...
And now, I can't, because you're gone, like Red...
No, somehow, you're still here...
X, Zero...
Thank you, for everything.
Take a break, you guys deserve it.
Actually, make sure that it's a long one, a really long one.
Ciel and the resistance can take care of the world now and for what they can't handle...
There's me.
I'll speak up, I will remind the world that I'm still here.
Me, Axl, the Kid, the prototype with a gun, I'll tell the world that I'm still here and that they don't have to rely on you two to fix the problems and if they still want to make you two clean up the mess that they made, they'll have to go through me!
So don't worry guys, everything's going to be okay, I'll be the Hero now.
I'll see you later, X, Zero.
Axl.