The Gator Wars was a division between the members of the Hive Mind who wanted to remove Lazorgator for being overleveled, and those who wanted to keep him. Because of this "war", four Pokémon were released and the lore changed from relying on Twitch Plays Pokémon Red Version to create lore, to No Gods. No Kings. Only 'Mons, and the idea of slaying the gods.
The First War
Starting on the third day of Twitch Plays Pokémon Crystal Version, AJ had already defeated all five Kimono Girls and received the HM for Surf. Just after this, Croconaw evolved into Feraligatr. Democracy kicked in shortly after and the Hive Mind replaced Scary Face with Surf. The day continued without any problems until they reached Olivine City, where a dispute erupted amongst the Hive Mind, some who believed that a overpowered Lazorgator was carrying the entire game and making it impossible for any other Pokémon to contribute. A anti-Lazorgator faction was formed afterwards and planned to release him or put him into the PC until AJ's other Pokémon had a chance to get stronger. This chaos continued for several hours as AJ was dragged all across Olivine City, even causing the release of a few Pokémon.
Finally, Feraligatr was deposited into the PC as a training session began in Route 39 but little progress was made due to the Gator Wars continuing. After some grinding the Hive Mind went back to the Poke Mart to get some more Poke Balls but they where sidetracked to the PC by some members of the Hive Mind who wanted to retrieve Gator. A battle for control breaks out against those who want him back and those who want him in the PC. According to lore, after The Admiral was released due to the Gator Wars, this caused Lazorgator to turn from the cute Pokémon to the godslayer it is today. In the end, Democracy was activated, successfully withdrawing Feraligatr from the PC.
The Second War
However during Day 4, another war for control breaks out between the Pro-Gator and Anti-Gator fractions in the Cianwood Pokémon Center. During the struggle, all Pokémon but Gator are deposited into the PC. AJ withdrew Zubat, Smoochum, and WWWEEE without any casualties and names Box 1 IRmn before heading towards Route 41. However after reaching Olivine City, another Gator War erupted. After much struggle, AJ heals his Pokémon and heads to the lighthouse. The Gator Wars continued with the Anti-Gator fraction becoming more powerful than ever before a compromise is suggested, to avoid having the PC, AJ returned to the Day Care to deposit Feraligatr. Of course, to do this shuffle, he had to use the PC anyway, and ended up with a party comprised of Brian, himself, Hoothoot, Shuckle, and Eevee. Wooper had been released in this battle.