well, at the end of X3, it says X will never find peace until he destroys zero, many years later in Zero 2, X loses his body and zero is still alive and kicking.
Command mission was good game, it was a fun RPG, but the story sucked. True to the series, Command mission was all about gameplay and some crack addicts made up the story.
I mean the things that they say! god!
Axl is the only one who doesn't say anything completely stupid! (then again, he doesn't say much)
and X is so gay for zero in that game. The scene where zero "returns from the dead" (he just got thrown far away, why'd he be dead? he always comes back anyway. really I'd think someone'd catch on already. Zero must die like every other week, he's like kenny!)
and there is no proof that zero was made before X was planned, nor that Bass was made after mega man. Wily just likes keeping ultimate warriors of destruction in capsules until the time is right.
Is it just me... or is Wily immortal? I mean, how does he talk to zero in the flashback? unless it was just a programm. But Isol from X6 does remind me a lot of Wily, and he does say "you truly are the strongest" right before he shuts down. that and command mission lead me to believe Zero is Bass. and Weil? that's German, and would be pronounced "vile". just add a "Y" and it's a bad pronounciation of Wily. I mean, the man has a freakin' boat shop in legends!
But then again. Capcom doesn't really know what they're doing when it comes to story.
And battle network is a completely different timeline.