I've been wondering about this, how in the world did Shadow loose his memory anyway?
It was never explained how Shadow survived the space colony ark battle.
the only thing i could sum up, is when Eggman took off in his ship he retreved Shadow, put him back in suspended animation, then when Rouge broke in on Sonic Heroes he was let out.

Was Eggman using Shadow to make the clone robots?

I still don't understand the memory loss though, after being suspended animation when Maria let him out, he could remember what happened after suspended animation.

I think it has to do with having the big fall and big events suddenly happening and stuff like that. How did he survive? Isn't he supposed to be the ultimate creation or something, so maybe he has some kind special characteristic which allowed him to survive that fall.