After Amy's kidnapping, Sonic Tails head off in the X Tornado to rescue her. Meanwhile, Knuckles gains most of the Master Emerald pieces and gets another vision of the past. After the vision, Knuckles puts the pieces on the altar and discovers the remaining pieces are in the Egg Carrier. Big Chris manages to find Froggy, but gets stolen by E-102 Gamma and They sneak into the Egg Carrier. After Gamma's success of getting Froggy, Eggman sends the other E-series into other places and orders Gamma to get the bird that's with Amy. When Gamma confronts Amy, she persuades him to help her escape. Knuckles hitches a ride with Sonic Tails and battles the Egg Carrier. After getting through the weapons, they enter the Egg Carrier where dangers await them.