I am pretty sure that him and Zack are friends at the start (probably still are)
but Cloud has left Shinra, stole a sword, has mako eyes and used a lampshade to get out of Shinra
I think Weiss or Nero are in a few chapters and possibly Genesis.
Reeve, Sephiroth and (Angeal?) are in it while Vincent and (Aerith?) are following him around Gaia
Also I think they head to the Gelnika or it's somewhere as Cloud decides to steal something from it.
Cloud breeds chocobo's (like lots of them)
Cloud dresses like before but this time hides his face as he doesn't want to anyone to know who he is.
I think he might send Sephiroth letters in hopes that he wont go crazy (which I don't think helps - too cryptic)
He fights Seph, saves Zack and the latter wants to know who this mysterious CS character is (even though he possibly knows it's Cloud anyway)
Thanks to anyone who knows this (I hope to god it was one story)