Brothers Josh and Jacob's lives are turned upside down when they awaken one morning to the sound of loud jet engines in the sky above them, and the sight of gigantic robots at their door, looking for them. Turns out, the boys had accidentally embroiled themselves in one of the nefarious Doctor Eggman's plots to take over Mobius and turn it into his own, personal utopia. Now, having been separated during the invasion, with no hope of getting home on their own, Josh's only hope rests in gathering up the Chaos Emeralds and using their combined powers to reunite himself with his little brother and get them back to Earth. Luckily, he won't be working alone.
As he learns to rely on Sonic's help to navigate through the strange, new world, Josh and his new friends must race to gather the Emeralds before Eggman can get his hands on all of them. But it won't be as easy, the Emeralds have taken on strange, new properties due to the experimentations of the mad Doctor. Josh, Sonic, and Knuckles, must quickly learn to adapt and overcome the new challenges that will face them if they hope to succeed.