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 New Villain Alliance 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, Jacob Nion.

The Hero Rebellion
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..