Amy Rose is grocery shopping in Station Square when three strange things happen: A Flicky lands on her, the Egg Carrier floats ahead, and ZERO the robot appears and chases her. She hides in Station Square Diner, where she decides to help the little Flicky find his family. She heads out and finds Sonic, and follows him. ZERO appears again, but Amy is preoccupied with taking a trip to Twinkle Park. ZERO chases her, as does Sonic.
ZERO catches Amy and takes her to Mystic Ruins, then takes her aboard the Egg Carrier. She is put in a cell, but E-102y comes by, asking for the Flicky. Amy talks to Gamma, which overrides his logic circuits, and he sets her free. She finds the Hedgehog Hammer game and plays a round to collect upgrades, then tries to escape by heading through Hot Shelter, with ZERO still in pursuit.
When she gets out, Tikal light shows Amy a vision of the past with Tikal and the chao. Amy goes outside where Eggman takes the emerald from the Flicky, and sends E-102 to fight Sonic and Tails. Amy stops them from killing one another, and Sonic sends Tails to take Amy to Station Square. Back in the city, Amy is still determined, and heads for Mystic Ruin's jungle, and over into Final Egg.
Once she gets out, she heads down to the Mystic Ruins raft and floats over to the crashed Egg Carrier. They find the Flicky's parents! ZERO appears, attacks the Flicky and holds a showdown with her. Angrily, she destroys him. The Flicky family fly away happily.