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Operation: EndGame was the name of Dr. Ivo Robotnik's final plan to wipe out Knothole and dispose of the Knothole Freedom Fighters, specifically Sonic the Hedgehog, once and for all. The plan had numerous phases and was nearly carried out to completion, but due to Snively Robotnik and Crocbot betraying the madman, the plan fell apart when the Ultimate Annihilator targeted only Robotnik, erasing him from existence.
When Sonic used Dr. Quack's invention - the Dream Watcher - in order to enter King Max's psyche to contact him during his coma, Robotnik managed to track the location of Knothole when he detected the Neutron Chip in Quack's device. While Sonic and the Freedom Fighters were absent from Knothole retrieving the Sword of Acorns, Robotnik sent Snively and a group of SWATbots to apprehend Dr. Quack and King Max, with the latter being replaced by an Auto Automatron. Fearing Sonic would interfere with his plans, Robotnik appealed to former Wolf Pack member Drago Wolf to set up Sonic as a criminal for Sally Acorn's death. Dr. Quack originally refused to work for Robotnik in helping assemble the Ultimate Annihilator, but when Snively brought Dr. Quack's wife and kids and threatened to roboticize them, he complied. (StH: #43, #50, SSS: #1)
The first phase of Operation: EndGame was to have Princess Sally Acorn killed while framing Sonic for her murder. Drago managed to convince Hershey Cat to wear a suit that made her look like Sonic, while the suit's eyes made it so anyone Hershey saw while wearing the suit looked like Snively. During one of their missions in Robotropolis, Sally ended up hanging on to a rope high above the ground. Hershey, believing it to be Snively, cut the rope, causing Sally to fall to what appeared to be her death. With everyone witnessing what they believed was Sonic killing Sally, the Freedom Fighters targeted Sonic as a fugitive. He was arrested and, instead of executed, was sentenced to the Devil's Gulag (StH: #47, #49)
While being transported to the Gulag, the transport ship was downed by SWATbots, allowing Sonic to escape. Warned by Drago, the King Acorn duplicate ordered Geoffrey St. John to hunt down and recapture Sonic. With the two best members out of the way (and Bunnie Rabbot and Antoine D'Coolette captured and sent to Downunda, Robotnik was able to enter Knothole and capture the town. (StH: #48, #49)
Originally, Robotnik planned to fire the Ultimate Annihilator and wipe out the hostages in Knothole. He first tested the weapon on an Overlander who had been captured from Mega Central, which proved the device worked. The only thing missing was the power source, a rare ore from Downunda delivered by his treacherous Sub-Boss Crocbot, who unknown to him was planing to kill him when the ore arrived in Robotropolis. Robotnik's plan started to backfire when Dulcy, able to realize Sonic was telling the truth, was able to convince Geoffrey, Knuckles the Echidna and Espio the Chameleon of Sonic's innocence. Sonic, Geoffrey and Knuckles returned to Knothole and liberated the town with Hershey attacking Drago, allowing Sonic to confront Robotnik. In Robotropolis, Sonic ran into Bunnie and Antoine, who were able to get free and reach the city via one of Crocbot's transports, intending on using the same plan Crocbot used to instead destroy the Ultimate Annihilator. The two were able to plant the bomb, but were unable to stop it before Robotnik obliterated Knothole from existence. Enraged, Sonic and Robotnik engaged one last time in a furious fight as the bomb went off, causing the weapon's energies to build up and be unleashed across Mobius. When reality snapped back, Sonic was transported to Knothole while Robotnik, the weapon modified to only affect his specific DNA, was erased from existence. (StH: #50, SSS: #6)
Upon returning to Knothole, Sonic learned that Sally had in fact survived the fall, but was in a coma and in a stasis chamber. As well, Knothole was not destroyed, instead trapped in a strange Zone three hours into the future. No longer a wanted fugitive as Dulcy had cleared his name, Sonic went to visit Sally and woke her from her coma with a kiss. (StH: #50, SSS: #6)
- The arc which Operation: EndGame was carried out was also called "End Game".
- It was later referred to by Dr. Eggman as "Project:Endgame" to Drago Wolf.
- Sally was originally planned to be killed off permanently during Operation: EndGame, until SEGA forced Archie to alter the story-line after furious backlash from fans, mostly those of the Sonic SatAM TV series.
- The original end to Operation: EndGame with Sally's death was briefly referenced as a possible alternate reality in the future (when Chaos Knuckles tried to alter the timeline) by having the Knothole Freedom Fighters visit her grave.
- In Sonic SatAM Dr. Robotnik had a final plan called "The Doomsday Project" it had similar concepts to Operation: EndGame and was possibly an inspiration for it as well.