Project Nintendo is the sequel to Project Sega. It is the second installment in the Project series.
After Sonic defeated Project Sega, Eggman Nega is flung into space and crashes back down. As he gets up, he realizes that he has landed in the mushroom kingdom and he sees the opportunity to create a new plan. Mario rushes to Green Hill Zone informing Sonic, Knuckles, Tails and the rest of them that Eggman Nega has invaded the Mushroom Kingdom. So Sonic, Mario and their friends work together to stop Nega once and for all.