The War of the Negaverse was a war between Dr. Eggman Nega and the Giygas clones, with Sonic helping the latter side. It took place in the Negaverse, obviously, and resulted in the extinction of the Giygas clones and disappearance of Eggman Nega.
After Eggman Nega killed most of the Giygas clones and enslaved all the humans in the Giygas Dimension, he renamed it the Negaverse and made it his personal stronghold. The remaining Giygas clones (Toonygas and Ronald McGiygas) decided to have their revenge. They summoned Sonic, because of his experience with battling all sorts of "Eggmen", and took him to the Negaverse.
Sending Out Sonic
Before attacking in full force, the Giygas clones (Ronald McGiygas and Toonygas) sent out Sonic to track down Eggman Nega and defeat him. Sonic did just that, and found Eggman Nega on top of a huge, snowy mountain. What Sonic did not know was that Eggman Nega's base was actually built into the center of the mountain, which was hollowed out inside. Upon spotting him, Eggman Nega challenged Sonic to a race down the slope instead of an actual battle. Sonic declined, and pushed him down the slippery slope, snowboarding after him. After Sonic had followed the rolling Eggman Nega, the latter disappeared through a hole in the side of the mountain. Sonic avoided this hole, thinking that it was dangerous to go near it, and reported to the Giygas clones that Eggman Nega had fallen down a hole and died an anticlimactic death...or did he?
Defeating Eggman Nega's Army
While Sonic defeated Eggman Nega, the Giygas clones preoccupied themselves with the demolishing of Eggman Nega's army. This army consisted of Teletubby Robots, autonomous Bombs, and Mecha-Zeldas. Although there were only two Giygas clones remaining, they managed to wipe out the entire army due to Ronald McGiygas' incomparable power and the Mecha-Zeldas' stupidity.
Eggman Nega's ReturnSome time later, Eggman Nega energed from his secret mountain base, alive. His legs and arms had been broken from his earlier fall, but he had obtained a suit of robot armor that allowed him to not only move normally, but to match the likes of Sonic and Ronald McGiygas in sheer power and skill. He hunted down Toonygas, killing him without a second thought.
End of the War and Outcome
After Ronald McGiygas finished annihilating Eggman Nega's entire army, he transported Sonic back to his home, the Sonic Islands. Although Sonic was reluctant to leave, Ronald McGiygas insisted that he would defeat Eggman Nega on his own. Once he found Eggman Nega and challenged him to a battle to the death, he was quickly outmatched due to Eggman Nega's prosthetic body armor. Knowing that he could not beat Eggman Nega in a duel, Ronald McGiygas transported him to what turned out to be the distant future. There, Eggman Nega met Silver, and the two of them became instant rivals. As for Ronald McGiygas, he used up the last of his energy during time travel and melted away into the time stream. However, he managed to survive for a while due to his sheer durability...until he was run over by a passing Time Machine and knocked into a nearby black hole.