Great Hero Purge

The Great Hero Purge referred to the efforts initiated by Sonic the Hedgehog to eradicate the heroes. It began with the deaths of Mario and Link at the hands of Sonic. Sonic, Ganondorf, Wolf, Meta Knight, Wario, and Bowser issued Order 66 to all Assist Trophies and Pokemon to execute the SSBB heroes. All of the other heroes were declared enemies all over the universe. Some heroes fought the Team Dark until their deaths, like Yoshi and Daisy. Right now, Peach, Pikachu, the Ice Climbers, and Heishiro Mitsurugi are preparing for a confrontation with Sonic, Darth Vader, and their companions, including Vader's secret apprentice, Galen Marek.

Mario's final battle
After the final death of Black Doom, Sonic told his companions that they were now ready to kill the Brawl heroes, but as Link turned around to leave, he was stabbed in the back by Meta Knight. Mario arrives and finds out that Sonic was actually planning to kill their own allies. Sonic then dueled Mario, while killing Link in the process. At the climax of the duel, Sonic overwhelmed Mario by grabbing, and crushing him, thus letting the heroic plumber fall to his death. After Mario's death, Sonic and his companions, with Wolf replacing Link, began the Great Hero Purge.

Order 66
Sonic and the other five fighters issued Order 66 to the assist trophies and pokemon to exterminate the heroes. The assisting teams followed that order without hesitation, nor question. As the extermination went on, many Brawl heroes were killed, except for five people: Peach, Yoshi, Pikachu, Popo, and Nana. The five went into hiding and searched for help. Sonic and his helpers could not let the survivors survive the purge. So they went on to hunt them down.

The Fall of G.U.N.
After the execution of Order 66, Peach, Pikachu, Yoshi, and the Ice Climbers asked G.U.N. to help them defeat Team Dark. G.U.N. agreed, and began to prepare for a hunt for the dark team. As the G.U.N. troops searched, they were overwhelmed by Shadow the Hedgeohg, another one of Sonic's assistants. He even attacked them on the space colony ARK. Some troops escaped the ARK, but the colony was taken over by Shadow and used the eclipse cannon to fire on Central City. Sonic and Shadow then flew to the G.U.N. Fortress, where G.U.N. were hiding. Shadow and Sonic however overwhelmed and destroyed part of the fortress. The two hedgehogs then fought the G.U.N. commander in his Diablon craft. The duo instantly killed the commander and fully destroyed the fortress, as Peach and her other friends looked on. This was known as the fall of G.U.N..

The Continuing Purge
During the purge, Sonic and his companions attacked the Eggman Empire, killing Dr. Eggman in the process. When Yoshi was teleported into the Halberd's Wii system, Sonic ordered Wario to go into the game console and kill Yoshi. Wario successfully killed Yoshi, and Team Rebel only had four survivors now. Later on, Sonic went on his own missions to get revenge on those who defy him. During one mission, he went to Yoshi's Island to kill the Shy Guys, then spotted another survivor, Princess Daisy. Daisy dueled Sonic while defending the Shy Guys, but she was killed by Sonic when he transformed into Super Sonic and ran through her just like a bullet. Sonic's two other missions were to assassinate a president and a skilled fighting Gonk Droid. Before his revenge plots could be complete, he met Darth Vader's secret apprentice, Galen Marek, who helped Sonic destroy the rest of the droid factory. This made Sonic's revenge plots complete, and thus, Galen was accepted into Sonic's team.

The Ultimate Confrontation
After the fall of G.U.N., Peach and her survivors found a swordsman named Heishio Mitsurugi and asked him to help defeat Team Dark and end the purge. Mitsurugi agreed to help, and helped them prepare for a confrontation with Sonic and the other villains. As Galen Marek kept on training, he would be ready to fight Mitsurugi's allies, and to one day overthrow Palpatine.

While Galen was training, Darth Vader explored and gazed upon the fiery mountains. There, he spotted three vikings and extinguished them, so did Mitsurugi. Only Vader and Mitsurugi were left, and they dueled to the death. After Vader and Mitsurugi's duel, the dark lord grabbed the japanese swordsman from behind, and stabbed him, killing him instantly. Peach, Pikachu, and the Ice Climbers would make their last stands after Mitsurugi's death.

End of the Brawl heroes
After Mitsurugi's death, Sonic decided to search everywhere for the surviving Brawl heroes. Meta Knight searched on the pirate ship for them, killing Claus in the process. Finally, Sonic and Meta Knight found the surviving brawlers, and began to fight them to the death. Meta Knight also killed the Ice Climbers and Peach, before Sonic can battle Pikachu in their final battle. After Peach and the Ice Climbers' deaths, Sonic and Pikachu dueled each other on the Galaxy Platform as Meta Knight left the two of them to fight. The fight lasted for a moment, until Sonic became Super Sonic and ran into Pikachu, killing the mouse pokemon instantly. This was finally the end of the SSBB heroes, and the continuation of the rise of the dark side. Team Dark would also change its name to Team Evil. Then, Team Evil went on to kill the rest of the surviving heroes and the remaining dark clones that have been a thorn on Team Evil's side for far too long.

Known Order 66 victims

 * Mario (before Order 66) - killed by Sonic on the Halberd.
 * Donkey Kong - killed by Sonic.
 * Link (before Order 66) - killed by Meta Knight in the Halberd hangar.
 * Samus - killed by Ganondorf.
 * Kirby - killed by Wolf.
 * Fox - killed by Meta Knight.
 * Marth - killed by Bowser.
 * Mr. Game & Watch - killed by Sonic.
 * Luigi - killed by Ganondorf on Spear Pillar.
 * Diddy Kong - killed by Wolf.
 * Zelda - killed by Meta Knight on Big Blue.
 * Pit - killed by Wario.
 * Falco - killed by Bowser in WarioWare.
 * Pokemon Trainer - killed by Sonic in Delfino Plaza.
 * Ike - killed by Ganondorf.
 * Snake - killed by Wolf on the Bridge of Eldin.
 * King Dedede - killed by Sonic.
 * Lucario - killed by Ganondorf in Smashville.
 * Ness - killed by Wolf.
 * Toon Link - killed by Meta Knight inside the Pokemon Stadium.
 * R.O.B. - killed by Wario on the pirate ship.
 * Olimar - killed by Bowser on Skyworld.
 * Captain Falcon - killed by Sonic.
 * Jigglypuff - killed by Ganondorf.
 * Lucas - killed by Wolf.

Subsequent Purge victims

 * G.U.N. Commander - killed by Shadow and Sonic.
 * G.U.N. President - presumably killed by Shadow.
 * Dr. Eggman - killed by Shadow inside the Lava Shelter.
 * Yoshi - killed by Wario inside the Wii System.
 * Daisy - killed by Sonic on Yoshi's Island.
 * Ruz Afar - killed by Darth Vader's secret apprentice in the Power Droid Factory.
 * Baloo - killed by Shere Khan.
 * Mowgli - killed by Shere Khan.
 * Blood Falcon - killed by Darth Vader's secret apprentice on Hoth.
 * Rosh Penin - killed by Jaden Korr during his betrayal.
 * Heishiro Mitsurugi - killed by Darth Vader.
 * Claus - killed by Meta Knight on the pirate ship.
 * Ice Climbers - killed by Meta Knight.
 * Peach - killed by Meta Knight.
 * Pikachu - killed by Sonic.
 * Taki - killed by Darth Vader's secret apprentice.
 * King Louie - killed by Ganondorf in Notre Dame.
 * Angol Fear - killed by Darth Vader's secret apprentice.
 * Talim - killed by Darth Vader's secret apprentice.
 * Staarkiller - killed by Darth Vader.
 * Zasalamel - killed by Darth Vader.
 * Darth Vaader - killed by Darth Vader's secret apprentice.

Known survivors as of the end of the purge

 * Unknown