The episode starts with Knuckles on the Floating Island rather upset at himself breaking the Master Emerald as he has another vision of the shrine in flames. Waking up quickly he decides that he can gather what is left of the emerald and takes off.
Back at Chuck's lab the X Tornado takes off into the air with both Tails and Sonic on board. Chuck stays back hopping they will be able to fin Amy and Tanaka says everything will be okay while Ella assures Cream that Amy is okay. Up in the air Sonic is worried about Tails' condition and as Sonic goes to leave the plane Tails convinces Sonic to work as a group as Sonic decides to ride on the outside of the plane.
Nearby Chris is wondering why Big has gone fishing and assures Chris that he knows what he is doing as Chris spots the X Tornado in the sky. Far down below the ocean though Eggman sits on his Egg Carrier as Amy screams to be let out, she looks around and sees nothing. She daydreams about cooking for Sonic and thinking they are getting closer together as she continues to daydream about being rescued by Sonic. Up in the control room Becoe and Decoe are arguing over using the microphone, as Eggman appears giving instructions to his four E-series robots to go after Froggy and bring it back to the plane. The four robots leave out the door with orders not to fail.
At the Mystic Ruins Knuckles heads inside to see many pieces of the Master Emerald grabbing the largest floating one he again encounters a vision. This time he finds himself standing on a dirt road before the shrine. Heading up to it he sees Tikal and the chao and watches as Tikal pleads with Chaos to help them. She then understands that they can leave but Chaos itself must stay put, she reassures the chao that everything will be fine. Tikal is taken up further on the shrine by the chao and glances around at the Chaos Emeralds before gazing on the Master Emerald. She learns the famous chant the emeralds are the 7 servers and the controller serves to unify the chaos. Knuckles stands behind her watching as his vision ends he stands before the present alter of the Master Emerald. Knuckles ponders what the vision was about and knows that it is something to do with the Master Emerald. He releases the shards that he has on the Master Emerald as it reforms still missing a single piece. The emerald then shows the Egg Carrier and he believes that it is a warning of Eggman.
Elsewhere the four E-series robots are searching through the grass to find Froggy as Gamma spots Chris and Big fishing. The other 3 believe they have found Froggy as Gamma continues searching. Hearing Big and Chris and seeing Froggy Gamma quickly takes off running. Becoe and Decoe recall the four robots as each as found a frog. Chris and Big chase after the four robots as the Egg Carrier rises from the sea. As the four robots board the ship Chris and Big follow them onto the carrier. The four robots argue who has the real Froggy. As Eggman inspects the first three frogs he is rather upset over the failure of the robots thinking that they are all failures.
Below Chris and Big wonder where to go as they head off through the interior of the ship. As Eggman continues to be upset he spots the frog that Gamma is holding and sees that it is the real Froggy and is proud of Gamma as he sends the other three robots into destruction. Eggman is rather proud of Gamma and orders it to retrieve the bird that Amy has. As Chris and Big explore the ship Gamma walks past them and the two look confused. Gamma then enters the wrong chamber to find Beta undergoing repairs he spots parts laying on the floor. Gamma concludes it is the wrong room and leaves entering the prison to find Amy and the bird. Gamma orders Amy to release the bird but Amy refuses. As Amy tells Gamma that Eggman cannot have the bird and she is not afraid of him, Gamma becomes confused and Amy uses her charm to try and get Gamma to release them. Gamma becomes confused saying it must obey Eggman and the bird escapes flying in front of Gamma. The robot goes into overload and decides to release Amy and the bird telling Amy to leave. Amy gives her thanks as the two run off quickly.
Meanwhile the Egg Carrier has taken off into the mountains while below Knuckles watches the ship fly overhead. The X Tornado lands next to him and he hitches a ride with Sonic and Tails. Eggman is rather happy until he learns the X Tornado is on pursuit. He begins firing on the plane as Tails uses his skills to dodge the assault while Knuckles and Sonic hang on for dear life. Eggman fires the master cannon of the Egg Carrier and Tails is just barely able to dodge the beam as he transforms the X Tornado into its battle armor mode complete with two giant fists.
Eggman orders the Egg Carrier to be transformed as it converts into its larger form. The three stand surprised at the transformed ship in a stand off position. As Eggman continues his assault Tails releases a giant shield from one arm and a sword from the other to destroy and block the missiles being launched at the X Tornado. Tails gets a little full of himself and Sonic has him cool down some. Becoe and Decoe accidentally release fireworks and celebrations under a warmer welcome order and Eggman orders them to switch into battle mode. As Tails goes to land he remembers that he forgot to landing gear for the current mode as the three crash into the Egg Carrier, ending the episode.