Air date: September 28th, 2003 (JP), March 27th, 2004 (US)
Continuing from A Dastardly Deed, Eggman now has six of the Chaos Emeralds, along with Chris Thorndyke as his hostage, and E-77 Lucky has called in to report he found the seventh one. As Eggman heads to Lucky's location in the Egg Fort II, Guardian Units of the Nation agents Topaz and Rouge the Bat pursue in a helicopter as Tails, Amy, Cream, Cheese, and Chris' grandfather, Chuck Thorndyke, head in that direction in the X-Tornado. Meanwhile, other G.U.N. agents are standing by with their secret weapon from Project Beetle to engage the Egg Fort II with.
Once Eggman reaches Lucky's location, he is interrupted from retrieving the final Chaos Emerald by Sonic, who is just about to accept it from Lucky when G.U.N. arrives with their secret weapons, the Beetles, which open fire on the Egg Fort II, despite Sonic's warnings that Chris is on-board. Eggman is able to deploy the Egg Shield just in time, only to become furious when he learns that the G.U.N. Beetles are built using his technology salvaged by them. He counterattacks with the Egg Beam Cannon, but the Beetles survive, and after Sonic catches Lucky when he's sent flying in the blast, Lucky hands over the seventh Chaos Emerald to Sonic. It is then Eggman decides he's done messing around and pulls out the heavy guns, transforming the Egg Fort II into the E-99 Eggsterminator (Egg Emperor in Japanese), powered by the other six Chaos Emeralds, allowing it to out-maneuver Sonic and badly beat him up. Neither the X-Tornado, nor Topaz and her fellow G.U.N. agents can get close, and the G.U.N. Beetles are quickly destroyed by the Eggsterminator.
Despite being battered, bruised, and clutching one arm with the other one, Sonic refuses to give up until he saves Chris, at which point, the Eggsterminator turns a bright orange color and begins going ballistic on Sonic, beating him to within an inch of his life, unnerving Eggman, and devastating Chris. Finally, unable to bear seeing Sonic being mercilessly beaten nearly to death, Eggman orders the Eggsterminator to cease its attacks and let Sonic go. However, the Eggsterminator delivers a final drop-kick to Sonic to send him into the sea and a watery grave, frightening Eggman, and leaving Chris horrified. It's too much for Chris to endure, and he's able to break free of his restraints and grab the six Chaos Emeralds, being badly burned in the process due to the Emeralds still having their energy being used to power the Eggsterminator. As a battered and weak Chris hugs the Emeralds tightly and refuses to hand them over, Knuckles arrives to rescue Chris and get revenge for being double-crossed by Eggman, but Rouge has already flown off with Chris. However, his struggling causes Rouge to drop him and leave the Emeralds to fall into the sea where Sonic and the seventh one are. Even without the Emeralds, the Eggsterminator still grabs Rouge and Chris and starts to crush them in its fist.
However, it never gets the chance to finish the job as the fist holding Rouge and Chris is suddenly disintegrated into shrapnel. That being the result of Sonic having been revived by the Chaos Emeralds and transformed into Super Sonic. Eggman does nothing to retaliate, knowing that with Sonic in his super form, Chaos Control is about to take place. As the still out-of-control Eggsterminator tries to retaliate with its remaining fist, Super Sonic blocks the attack and soon reduces the Eggsterminator to a fiery wreck in the span of a few seconds, before causing Chaos Control to happen, worrying Topaz, while Chuck would be honored to return to Sonic and his friends' home world with them.
In the void of Chaos Control, Super Sonic is with Chris, and uses his powers to heal Chris of his wounds, before sharing a hug with Chris before disappearing, as Chris pleads for him not to go. However, instead of Sonic taking everyone home, he brings Angel Island and the Mystic Ruins to Station Square instead. Shortly thereafter, Eggman, having crashed on Angel Island following the Eggsterminator's destruction, finds a mysterious stone tablet, while Chris is soon relieved when Sonic, now back to his normal self, appears and gives a thumbs-up to show he's back.
- Sonic: (chuckles) Hi there again.
Countdown to Chaos provides examples of:
- Big "NO!": In the English dub, Chris screams this upon being forced to watch helplessly from his restraints as the Eggsterminator sends Sonic falling into the ocean with one final drop-kick.
- Cliffhanger: The episode ends with Angel Island and the Mystic Ruins being warped to Earth through Chaos Control, along with Eggman finding a stone tablet from Angel Island.
- Darker and Edgier: Not as bad as other episodes by a long shot, but by Season 1 standards, this is the darkest episode in the series considering Sonic almost gets killed by E-99.
- Do Not Adjust Your Set: In the Japanese version, Dr. Eggman warns viewers that they "Won't be able to keep up" if they change the channel and miss Eggman's robot transform.
- Dub Name Change: In the Japanese version, Eggman's ultimate robot is known as E-99: Egg Emperor. The 4Kids version calls it Eggsterminator (which actually clears confusion from it and the Egg Emperor boss from Sonic Heroes). Also, Lucky is just called E-77 in the Japanese version.
- Even Evil Has Standards: When the Eggsterminator goes ballistic with beating Sonic to a pulp, Eggman can't bear seeing his arch-enemy beaten nearly to death and tries to talk his robot down. It works, but not without the Eggsterminator delivering a final drop-kick first to ensure Sonic's demise.
- Golden Super Mode: The first animated appearance of Sonic's Super Mode from the power of the Chaos Emeralds.
- Knight of Cerebus: The Eggsterminator holds the honor of being one of the few enemies to present Sonic dying as a possibility, and it really shows when Chris starts tearfully crying out for the No-Holds-Barred Beatdown that it's delivering to Sonic to stop, and Eggman tries to get it to stop as well.
- Know When to Fold 'Em: Eggman stands down once he realizes Super Sonic is about to induce Chaos Control, not taking any further steps to try and get the Eggsterminator to retreat or fight back on his command, knowing it is futile with Sonic in his Super Mode. All he does is sit and wait for the inevitable as Decoe and Bocoe come to the realization themselves...Eggman: LET CHAOS CONTROL BEGIN!
- Not So Invincible After All: Sonic shows that despite being quite a powerhouse, even he can't defeat E-99. Until he reveals his...
- Super Mode: Sonic making his first transformation into Super Sonic in his animated history.
- Wham Episode: Sonic reveals his Super form for the first time and causes a big Chaos Control that brings both Angel Island and the Mystic Ruins to Earth.
