God's War (Ishinomori's original memos, possible spoilers)
I came across Ishinomori's original planning notes for the arc sometime back, although they're all in Japanese and very fragmentary. It may take a while for translation, and I'm uncertain if they should be widely circulated about. The Italian fanbase for Cyborg 009 had known of these notes for years, but did not like sharing them possibly out of netiquette concern. These memos were published in some limited edition book by Kadokawa years ago, which is how they'd gotten out.
With thumbing through them, I'm wondering if a page or section could be dedicated to the differences between Ishinomori's notes and the posthumous novel and manga. I'd want to respect Ishimori Pro's wishes, though, whatever they'd might be.
From the looks of it, "God's War" had a few of its character-centric chapters completed (if only in draft form), while things like the last battle against the Gods were left unwritten or only had some vague plot/concept notes. Ishinomori was to have World War III and nuclear war going on in the background. The ultimate fate of the team seems to have been the same, although that too is very vague.
It's important to keep in mind how his passing not only resulted in some of the plot having to be altered (the cartoon!Ishinomori was envisioned as a 74-year old man living in the year 2012), but that his timeline for "God's War" also got tweaked due to later events. Since the manga would have been published in 2000, his ideas of what the years 2001-2012 would be like would no longer really apply in the current decade.
From the look of things, the whole controversial "cyborgs get mutilated and physically upgraded first" subplot wasn't anything that was anywhere in Ishinomori's drafts, and that the team would have only gotten their Super Warrior/"Psi-borg" powerups. That, and while 001, 003, and 009 are still the last three left standing in the battle, their final stand against the Gods looks to have been very different in the outline (and of course, the vagueness of the other team members' deaths probably encouraged Onodera and co. to get gruesome)
Ishinomori makes it a point that the characters' names we see in the arc are only pseudonyms as well, and that the "real" 00 team members' names differ greatly from the names we're used to. ie: Jet is not Jet, Francoise is not Francoise, and so on. The only actual name he revealed in the notes would be "Ivan Torsky" for 001 (which Onodera did incorporate into the manga).
It's quite the read. The OVA version is basically an abridged version of some of the chapters that Ishinomori outlined, only adapting from the prologue, Joe's chapter, and then having Ivan power up the rest before they go off to face the Gods. It also appears that the Japanese fanbase was expecting an actual conclusion/follow-up to the OVA (since the three episodes were subtitled "Prologue"), but it never came.