- Plot: Karl Bollers and Ken Penders
- Script: Karl Bollers
- Pencils: Ron Lim
- Inks: Andrew Pepoy
- Colors: Josh and Aimee Ray
- Letters: Jeff Powell
- Editor & Art Director: J. F. Gabrie
- Managing editor: Victor Gorelick
- Editor-in-chief: Richard Goldwater
In Station Square, Sonic tells the Freedom Fighters about his recent battle with a water monster. Mayor Bullyani thanks Sonic for his help. Sonic then asks him if this happenes often, which the Mayor denies, but he also states that this reminds him of a legend he once heard about a being known as Perfect Chaos. Nate Morgan interrupts to ask if anyone had seen Amy, but the others answer that she has not been seen since yesterday. The group then discovers that her bed had not been used. Sonic suspectes that Amy's disappearance and the water monster were connected through Dr. Eggman. The Mayor remarks that he hasn't seen Eggman, but Sally rebuffs this. Bunnie and Antoine are sent out to search for Amy in the city, to no avail, even with Bunnie extending her legs so that she and Antoine could see over the humans.
Sally, Nate and Nicole visit the library to find information on Chaos. They find out that Chaos was trapped within the Black Emerald by Chao who transformed themselves into Super Emeralds. Nate claims to have used one in the past to create the Ring of Acorns, from which Amy has now harnessed the power. Sally is worried about Amy, as Eggman could use these powers to revive Chaos. Sonic and Tails head to the Mystic Ruins to search for Chaos, but fail to notice the monster following right behind them.
Sonic and Tails fly over Knuckles in the Tornado, who heads over to greet them. Sonic asks Knuckles why he's in the Mystic Ruins, questioning the presence of a little ball of light following Knuckles, to which he responds "Oh that? Long story!". He goes on to state that he came here to find the Master Emerald shards, but is then ambushed by Chaos before he can continue. Sonic tries to fight back by running around it, while Tails askes Chaos why it was attacking. Chaos doesn't answer, but rather attempts to hit Tails, who barely manages to dodge. Knuckles slams Chaos onto a rock in retaliation, but is then counterattacked, causing him to drop the Emeralds. Tails notices two shards of the Master Emerald nearby and grabs them, but trips and drops the shards, which are retrieved by Eggman. He gives the shards to Chaos, causing it to undergo another transformation.
Eggman orders Chaos to attack the heroes, but they manage to dodge its attacks. While they fight Chaos, Eggman then boasts about his plan to feed him the 7 Super Emeralds in order to destroy the Hidden City of the Ancients and create his own city known as "Robotnikland". The three heroes then work together to counter Chaos' attacks. Knuckles punches the ground, causing Chaos to be temporarily stunned, while Tails kicks up sand with his tails, and Sonic runs circles around Chaos, heating the sand to form a glass ball surrounding Chaos. However, the Chaos manages to break free by splashing around at high speed, and makes off with Eggman. Sonic wants to chase after him, and Knuckles tells him to go ahead; as he has unfinished business to take care of.
Elsewhere, Big follows Gamma's scent in an attempt to find his friend Froggy, but the trail ends in the middle of a river. He doesn't have much time to dwell on this as the Egg Carrier rises from directly underneath him.
Sonic and Tails approach the airborne Egg Carrier in the Tornado. They manage to avoid the missiles by transforming the plane into its jet form, but they are forced to land, with Tails realizing he forgot to add landing gear for the second mode. As Sonic and Tails make an explosive entry, Knuckles sets off warn the citizens of the Hidden City about Eggman approach. Eggman, however, has headed that way to demonstrate the Egg Carrier's drill. Sonic and Tails make their way to the bridge, only to find Gamma and Eggman waiting.
Gamma opens fire on Sonic and Tails, while elsewhere, Knuckles receives a vision from Tikal, revealing that the Tornado is powered by a Super Emerald. Realizing that Chaos will be after it, Knuckles decides to intervene, as he finds himself on the Egg Carrier, after the vision ends.
Meanwhile, Sonic manages to fend off Gamma by deflecting one of his lasers back at him. He then prepares to finish him off, but Amy steppeds in, impeding Sonic from going further saying Gamma is her friend. Meanwhile, Big has found Froggy, who spits out the Emerald when Big hold him. Big picks it up, and notices it is similar to one he found earlier. Eggman then appears, and snatches both the emeralds, giving them to Chaos.
Tails notices that the Egg Carrier was losing altitude. Sonic tells him to get to safety with Amy while he finishes the fight with Eggman. While searching, he finds Big, who is stunned at seeing Froggy pursue the Emeralds inside Chaos, getting himself stuck inside the creature. Big manages to pull Froggy out with his fishing pole and walks away with him. by which point Knuckles arrives.
Eggman appears and uses several Ice-bots to freeze Sonic and Knuckles in their tracks so that the will be easier for Chaos to digest. Chaos then attempts to eat Knuckles, who is frozen, and can do nothing about his situation. Sonic however, notices that Chaos can not swallow the ice, so he flings an Icebot into Chaos, causing it to freeze solid and release Knuckles. After freeing themselves, Sonic and Knuckles smash Chaos into ice fragments, setting off a chain reaction that destroys the Carrier. Sonic head for the bi-plane, but finds it missing, as it was taken by Big. Just then, Knuckles grabs Sonic and glided of the carrier before it explodes.
When they return to solid ground, the heroes part ways, with Knuckles traveling back to the Mystic Ruins to continue his search for the Emerald shards, Sonic, Tails and Amy returning to the city to meet up with the other Freedom Fighters, and Big crash-landing the plane, heavily damaging it. Eggman however, is shown approaching Shrine Isle, with mysterious a blue ooze attached to the side of his Egg Mobile.
- Amy Rose
- Big the Cat
- Dr. Eggman
- E-100 Alpha
- E-102 Gamma
- Ice-bot (only appearance)
- Knothole Freedom Fighters
- Knuckles Clan (Portrait)
- Knuckles the Echidna
- Mayor Bullyani
- Nate Morgan
- Shadowbot (mentioned)
- Prime Zone
J. F. Gabrie urges Sonic to come and meet his fans but instead Sonic is glued to the T.V., playing Sonic Adventure. Gabrie eventually gives in and asks Sonic to reset for two players.
- This issue was part of the Sonic Adventure tie-in story arc, which also included Sonic the Hedgehog #79-#84.
- This is the first issue where Tails is the same color as his game counterpart.
- Judging by the preview cover, the art of Tails, Knuckles and Dr. Eggman were originally from the promotional CG artworks made for the video game Sonic Adventure.
- This is the first time Robo-Robotnik is called Eggman.
- An editor's note on the panel where Gamma escapes the Egg Carrier mentions that Gamma's adventures continue with his in-game story. However, Sonic Universe #3 reveals this was not the case.
- Amy's eyes are miscolored yellow on the cover. Strangely, they were correctly colored green in the preview cover.
- Tikal's name is spelled "Tical".
- Page 22 has two panels that were drawn by Patrick Spaziante. Spaz is not credited for these panels in any printing of this story.