Sonic told the Freedom Fighters about his recent battle with a water monster. Mayor Bullyani thanked Sonic for his help. Sonic then asked him if this happened often, which the Mayor denied, but he also said that this reminded him of a legend he once heard known as Perfect Chaos. Nate Morgan interrupted to ask if anyone had seen Amy, but the others answered that she had not been seen since yesterday. The group then discovered that her bed had not been used. Sonic suspected that Amy's disappearance and the water monster were connected through Dr. Eggman. The Mayor remarked that he hasen't seen Eggman, but Sally rebuffed this. Bunnie and Antoine were sent out to search for Amy in the city, but this turned out unsuccessful, even with Bunnie extending her legs so that she and Antoine could see over the humans.
Sally, Nate and NICOLE visited the library to find information on Chaos. They found out that Chaos was trapped within the Black Emerald by Chao transforming themselves into Super Emeralds. Nate claimed to have used one to create the Ring of Acorns, from which Amy has now harnessed the power. Sally was worried about Amy, as Eggman could use these powers to revive Chaos. Sonic and Tails went to the Mystic Ruins to search for Chaos, not noticing that the monster was right behind them...
Sonic and Tails flew over Knuckles in the Tornado and he went over to greet them. Sonic asked what Knuckles was doing there, questioning the presence of a little ball of light. Knuckles told them it was a long story. He stated that he was here to find the Master Emerald shards, but he was then attacked by Chaos before he could say anything else. Sonic tried to fight back by running around it. Tails asked Chaos why it was attacking, but the monster tried to hit him. Knuckles tacked Chaos onto a rock in retaliation, but it then attacked back, taking his Emeralds with it. Tails noticed two shards of the Master Emerald nearby and attempted to grab them, but he tripped and the shards were retrieved by Eggman. He gave the shards to Chaos, starting another transformation.
Eggman ordered Chaos to attack the heroes, but they managed to dodge its attacks. Eggman then boasted about his plan to feed Chaos the 7 Super Emeralds in order to destroy the Hidden City of the Ancients and create his own city. The three heroes then worked together to counter Chaos' attacks. Knuckles punched the ground, causing Chaos to be temporarily stunned. Tails kicked up sand with his tails, and Sonic ran fast enough to create a glass ball around Chaos. However, the creature managed to break free by splashing quickly, and made off with Eggman. Sonic wanted to chase after him, and Knuckles allowed him to go ahead; for he had unfinished business.
Elsewhere, Big followed Gamma's scent in an attempt to find his friend Froggy, but the trail ended in the middle of a river. He didn't have much time to dwell on this as the Egg Carrier appeared from directly underneath him.
Sonic and Tails approached the airborne Egg Carrier. They managed to avoid the missiles, but they were forced to land. Just then, Tails remembered something: his plane did not have landing gear. As Sonic and Tails made an explosive entry, Knuckles received a vision from Tikal and was told to warn the people of the Hidden City. Eggman, however, has headed that way to demonstrate his drill on the Egg Carrier. Sonic and Tails made their way to the bridge, only to find Gamma and Eggman waiting.
Gamma started attacking Sonic and Tails, while elsewhere, Knuckles received another vision from Tikal. Tails had a Super Emerald in his bi-plane and Chaos was after it. Knuckles decided to intervene and found himself on the Egg Carrier, but he shook this off and went off to find the Emerald.
Sonic managed to fend off Gamma by deflecting a laser back at him. He proceeded to finish him off when Amy stepped in, impeding Sonic from going further. Meanwhile, Big had found Froggy, who had coughed up an Emerald. Big noticed it was similar to one he'd found earlier. Eggman stepped in and snatched both, giving them to Chaos.
Tails noticed that the Egg Carrier was losing altitude. Sonic told him to get to safety with Amy while he finished the fight with Eggman. While searching, he found Big, who was stunned at seeing Froggy pursue the Emeralds inside Chaos, getting himself stuck. Big managed to get Froggy out with his fishing pole and walked away with Froggy, by which point Knuckles had arrived.
Eggman appeared and used Icebots to freeze Sonic and Knuckles in their tracks so that they would be easier for Chaos to digest. Chaos then attempted to eat Knuckles, who could do nothing about his situation. Sonic noticed that Chaos could not swallow the ice, so he flung an Icebot into Chaos, causing it to freeze up and release Knuckles. After freeing themselves, Sonic and Knuckles smashed Chaos into ice fragments, setting off a chain reaction that destroyed the Carrier. Sonic headed for the bi-plane, but Big beat him to it. Just then, Knuckles grabbed Sonic and glided out of the place.
Knuckles traveled to Mystic Ruins to continue his search for the shards. Sonic, Tails and Amy returned to the city to meet up with the Freedom Fighters. Big crash-landed the plane, destroying it. Eggman was still out there, with a blue ooze on the side of his personal carrier.