Last time on SONIC.NES! Super Somari finishes off NES, finally lifting the curse that's been on him and his friends, allowing them to rest in peace at last. However.. Somari soon realized this wouldn't be over yet, as the Queen who imprisoned him is still looming. Somari then goes off to train at Battikh's Planet to prepare to face her, while Taluigi's tasked to look after South Island.

Queen Microlite drags Huang's soul back into his vessel, twisting and mutating him to be her servant and knight in shining armor, Nescaliburn, a pure evil empty husk of who Huang used to be. She also drags Hayami's soul into the game, just to torture her. Hayami and (mainly) Taluigi now have to work together to survive from Nescaliburn and the Queen's various other monsters!