The Greyhawk Wars refers to both an in-universe period in the Greyhawk setting for Dungeons & Dragons and to the splatbooks and adventures that relate to that time period. Essentially, it was the Greyhawk equivalent of the Time of Troubles or the Wrath of the Immortals: a Canon Catastrophe intended to give TSR - meaning You Know Who - the excuse "they" needed to rewrite the setting and First Edition generally into something more to her liking. Or, at least, to something that wasn't to Gary Gygax's liking. That would end up as the box set From the Ashes - but we are getting ahead of ourselves.
TSR laid the groundwork in 1991 with two World of Greyhawk Swords modules: WGS1: Five Shall Be One by Carl Lynwood Sargent and WGS2 Howl from the North by Dale Henson. These described events leading up to the war. The third module was reworked into Greyhawk Wars, a strategy war game that led players through the events, strategies, and alliances of the actual war. A booklet included with the game, Greyhawk Wars Adventurer's Book, described the event of the war.
Although WGS1 can be played without reference to metaplot, Greyhawk Wars cannot - more exactly, it is the wrecking ball to the old metaplot. If you didn't play this, your campaign was stuck with the 1e material and timeline; or, with From The Ashes. If you did play this, you're basically watching Tanya The Evil, or playing Diplomacy or Risk, for all the difference it made to canon. It didn't matter much which, to Lorraine. As long as TSR got to start over and to delete Gygax and all his works.
As to the fluff: In 582 CY (six years after Gygax's original setting of 576 CY), Iuz started a conflict that gradually widened until a war ensued that affected almost every nation in the Flanaess. Two years of horror and then stalemate brought negotiators to the city of Greyhawk, which is why the conflict became known as the Greyhawk Wars.
On the day of the treaty-signing, Rary — once a minor spellcaster created and then discarded by Brian Blume, but now elevated (by TSR diktat) to the Circle of Eight — attacked his fellow Circle members, aided and abetted by Robilar. After the attack, Tenser and Otiluke were dead, while Robilar and Rary fled to the deserts of the Bright Lands. This sets up WGR3: Rary the Traitor.
Rob Kuntz, original creator of Robilar, objected to this storyline, since he believed that Robilar would never attack his old adventuring companion Mordenkainen. Although Kuntz did not own the creative rights to Robilar and no longer worked at TSR, he unofficially suggested an alternate storyline that Robilar had been visiting another plane and in his absence, a clone or evil twin of Robilar was responsible for the attack. In Gygax's setting, the major conflict had been between the Great Kingdom and the lands that were trying to free themselves from the evil overking. In Sargent's magical realm, the Great Kingdom storyline was largely replaced by the major new conflict between the land of Iuz and the regions that surrounded it. Southern lands outside of Iuz's were threatened by the Scarlet Brotherhood, while other countries had been invaded by monsters or taken over by agents of evil. Overall, the vision was of a darker world where good folk were being swamped by a tide of evil.
Alternatively all this was bullshit and didn't happen, and indeed many grognards merrily kept playing pre-Wars campaigns all through the 1990s in protest. The Internet (kicking off around this time) did its part in keeping "out of print" 1e modules in circulation, along with fan websites in how to expand on all that 1e lore. Who knew that nerds know how to work a fucking computer??
Everyone kissed and made up under Wizards Of The Coast when they put out the Living Greyhawk campaign. Still 2e rules (for a couple years), and we're not here to assure you that all of the newer modules and supplements were perfect; but it did get the job done as far as reconciling the neckbeards.