After obtaining the Chaos Emerald from Knuckles, Sonic continues to train with Emerl hoping to improve the robot's battle skills. However, Tails is determined to run a full diagnostic scan on Emerl, but needs to access the Central Lab to do so. Sonic let's Tails take Emerl to the Lab, but a stubborn security guard denies access to the area. Uncertain what to do next, Tails is approched by Rouge the Bat, who offers a Lab Pass if he can win a battle against her.
Once inside the Lab, Tails finally runs his inspection of Emerl, and the results are shocking. Accessing highly restricted data, the Lab's security systems are activated and suddenly Tails finds himself surrounded by a small army of Guard Robos. Things go from bad to worse as Shadow the Hedgehog arrives in yet another attempt to destroy Emerl.
Tails and Emerl escape Central City and reach the safety of Holy Summit, but Knuckles the Echidna isn't very thrilled to see the robot again. Following a rematch, Tails convinces Knuckles to return to Emerald Town with him but Chaos Gamma arrives also looking for a fight. Knuckles keeps Gamma busy as a distraction so Tails can escape and meet back up with Sonic...