- "Eggman Empire": Up until now Sonic the Hedgehog and Doctor Ivo "Eggman" Robotnik have been fighting for one hundred and seventy four issues. Every time they've fought, Sonic has found some way to win the day. This issue, however, Dr. Eggman pulls out all the stops and you'll never believe what happens. It's a 175th anniversary issue fans can't miss and one that Sonic may prefer to forget!
Above Knothole Village, a mysterious armada prepares to send out two robots below to "...end this silly little war." Meanwhile, at Freedom HQ, the Freedom Fighters–Sonic the Hedgehog, Sally Acorn, Rotor Walrus, Miles "Tails" Prower, Amy Rose, and newlyweds Antoine and Bunnie D'Coolette–along with Rouge the Bat and the Chaotix–Knuckles the Echidna, Vector the Crocodile, Mighty the Armadillo, Charmy Bee, Saffron Bee, Ray the Flying Squirrel, and Julie-Su–are relaxing after a most recent wedding. Knuckles then urges the rest of the Chaotix that they should search for Espio the Chameleon, as he's been missing since the ceremony. Julie-Su tries to comfort him that Espio will be fine, but Knuckles still believes something bad happened to him. Rouge then flirts with Knuckles, saying she will help him find Espio, making nearby Julie-Su ticked.
While Julie-Su and Rouge trash-talk each other, Sally comes in and tells Sonic that things have been quiet lately. Sonic then complements, saying that things have never been better, as families are reuniting, Knothole is becoming a booming city, and most of the villains are locked away. Sonic then goes as far as to say that they will be able to topple Eggman's empire one day. He then worries about Tails, as he has been acting different, as if he has been keeping something from Sonic. Tails then checks up with Nicole and asks if she is good enough to run a diagnosis in her systems since Snively sabotaged their systems sometime ago. Rotor then asks Tails if he's alright, since these past weeks for him have been rough, including a certain occasion with Fiona Fox and Tommy Turtle's passing. Tails admits it has been rough, but if he wants to prove himself as a Freedom Fighter, he will need to experience those scenarios. But Tails also tells Rotor that he got his family back not too long ago, and the two cheer, only for Nicole to report that they are under attack.
Suddenly, Snively in his beater tears through the roof, which causes several rocks to fall of the Freedom Fighters and the Chaotix. Rotor pushed Tails away from one, only for Rotor to hurt his back with a rock. Then, several Chaotix and Freedom Fighter members are vaporized by Snively, commenting that this is "...just like fish out of the water." Sally tells Bunnie to take care of Snively, but Snively's Beater grabs Bunnie and she is vaporized quickly. The remaining heroes include Sonic, Mighty, Tails, Amy, and Knuckles. While Mighty, agitated for Snively taking Ray, yells and rips off Snively's robotic arm, Mighty is vaporized, but the four remaining heroes stand back and try not to get vaporized. Sonic then runs towards Snively, only for him to self-destruct his robot, as he quoted that it "...was only a distraction." The three other Freedom Fighters then tell Sonic to go to Knothole, as Snively meant Eggman is attacking the city. Sonic then runs to Knothole, only finding the city burn to the ground. Sonic finds many locations, including the Lake of Rings and Chuck's Chili Dogs, destroyed by Eggman's forces. Sonic notices Castle Acorn is still standing and he quickly runs over there to save the House of Acorn, only for the castle to explode right in front of him. Eggman, in his Egg Beater robot, then confronts Sonic after walking away from the explosion.
Sonic, in frustration and disbelief, tells Eggman that his family, friends, and city are gone because of him. Eggman, however, tells Sonic that he and Snively transported his friends to the Egg Grape Chamber, where there "...it will all end." Sonic then reminds Eggman that Snively did not capture him, but Eggman told the hedgehog that he told Snively to leave Sonic for him. Eggman then attacks Sonic with missiles and a checked-sphere. While Sonic avoids the missiles, Eggman reminds Sonic that after many failures to save his friends, including Tommy Turtle and Sir Connery, and how he never deroboticize his friends, even his own father. Eggman then goes even personal, as he tells Sonic that his love-life has switch between Sally to Mina to Fiona, and Eggman questions Sonic why he's all alone right now. Sonic tells Eggman to shut up, but Eggman, bemused at Sonic for his witty comeback, wants Sonic to make some effort for their last battle, as Eggman called it. Sonic replies that Eggman thinks that this war is just a game, but Eggman recalls that he thought Sonic's resistance would stand up against his empire.
Eggman then tells Sonic that even though the world fell to him so easily, he kept the Freedom Fighters to entertain himself because he grew tired of taking over the world. Sonic then calls him a liar and the hedgehog replies that Eggman has tried–and failed–to beat the Freedom Fighters in the past. But Eggman then admits that although the Freedom Fighters have won more battles than he has, but asks Sonic if Mobius is any more free than it was years ago, during the Great War or even his coup d'etat. Eggman goes further on saying that because of the Freedom Fighters being powerless, King Maximillian Acorn would have never contacted the heroes, the very reason why this invasion happened. Sonic is then hit by Eggman, and the doctor commands Sonic to get up and continuing fighting him. Eggman then fights Sonic some more, telling the hedgehog that he was finished even before the Egg Fleet was made. The doctor goes on, as he has made the battle suit he's fighting Sonic with to out-match Sonic's speed, strength, and skill and that even with all of the Power Rings Sonic absorbed, Eggman can now toy around with Sonic even more. Eggman then tells Sonic that "...We've reached your limit."
An agitated Sonic repeats what Eggman said, and the hedgehog runs all the way across the Northamer. Eggman asks Snively to track down Sonic and how he can run that fast, as they have never seen Sonic run this fast before. Sonic, at the east coast, now brought on the emotional edge through his anger and desperation, is preparing a Figure-Eight Peel-Out move to defeat Eggman. Sonic then charges at Eggman as he unleashes his true speed. Snively warns Eggman about Sonic, and Eggman puts up his shield in front of him to minimize the damage that will be done by Sonic. Sonic then pushes Eggman back to the ruined-Castle Acorn, telling Eggman if that was enough limit for him. Eggman then gets back up, and tells Sonic he is upset for making a dent in his shield, the only damage Eggman took from Sonic's speed. Eggman then takes down Sonic easily, by telling him that he is still not stronger, smarter, nor faster than him. Sonic is then finally defeated by Eggman, a first in the empire's history. Eggman tells Sonic that he's going back to New Megaopolis, where he will freshen up and ready to make the citizens of Knothole into his fuel for his city. Eggman then gloats at Sonic, saying him to run across Mobius to find a new Freedom Fighter group, but he never will. Eggman continues on and tells Sonic to keep running across the world, but never to run "...from the humiliation of today." Eggman then throws Sonic on the ground and returns back to the Egg Fleet, leaving Sonic stranded in the middle of the destroyed Knothole. Tails then finds Sonic several minutes later and tells Sonic that they were able to dig themselves out of the ruined-Freedom HQ. Tails and Sonic look at Knothole and realize the damage that was done. But Sonic, however, tells Tails that he has a plan; a plan to save the Freedom Fighters before time runs out...
- In the beginning of the comic, Vector and Mighty are seen playing a Nintendo GameCube. The console is noticeable on the television, as well as the design of the controllers that they are holding.
- This issue featured one of the first times Dr. Eggman totally defeats Sonic.
- The friction between Sonic and Tails is mentioned in this issue, foreshadowing their eventual fight in Sonic the Hedgehog #178-#179.
- This is the first and so far only landmark issue in which the cover art does not make any note of the fact that it's a landmark issue in any form.
- In the early drafts for this issue, E-123 Omega would have taken Snively's role by carrying out the assault on Freedom HQ, and would have killed a still-living Tommy Turtle before fighting Bunnie Rabbot and eventually Sonic himself. But due to issues with Sega, these events were withdrawn and Omega did not appear until almost two years later in Sonic Universe #3.
- When Mighty rips off the arm of Snively's Beater, the detached left shoulder is gray instead of green.