During January, two mysterious meteorites falls down on the Mushroom Kingdom. They're multi-colored diamonds. When E. Gadd discovers that these diamonds is centuries old, they decide to keep them in the museum for further study. Months later, in the summer, a mysterious blue spikey being and a two-tailed creature fall from the sky. The blue being goes by Sonic, and the other by Tails. They explain they, and their friends were fighting their nemesis, Doctor Eggman, who has an invention that can conquer all dimensions. The machine overloads, and sends them all across the Mushroom Kingdom. Mario, Luigi and Princess Peach decide to let them stay until they're friends are found.
Two months later, Wario and Waluigi are hired by Bowser to steal a Chaos Emerald, which were the mysterious diamond meteorites, from the museum, so Bowser can put in his collecton. Sonic intervenes and manages to get one, but the Warios successfully get away with the other one. When they return, a giant metallic airship falls from the sky. The airship is the Egg Carrier, and it's owner Doctor Eggman, at first, does not take kindly to Bowser, and his son. But after leanring that Sonic is also in this dimension, he makes amends, and makes a deal with Bowser. If Eggman assists Bowser with kidnapping Peach, Bowser must help Eggman find the rest of the Chaos Emeralds. Mario and Sonic must stop these two villains before its too late.
