To get back the seven Chaos Emeralds from Dr. Eggman, Sonic and his friends manage to take the Blue Typhoon and go on a journey to the planet Skaro, where they help the peace-loving Thals battle the evil Daleks.

After Sonic and his friends traveling to Skaro, a month later, The Daleks have come to invade Mobius for revenge. This time they are using not just the Master Emerald and the Chaos Emeralds, but the Sol Emeralds, the Super Emeralds, Great Emeralds, Fire Emeralds, and the Chaos Crystals.