On the Floating Island, Sonic the Hedgehog, Miles "Tails" Prower and Knuckles the Echidna are deciding what to do with the crystalised statue of Robotnik (from the events of Order & Chaos). Sonic deduces it's up to Knuckles to sort things out, since Robotnik absorbed his Chaos Emeralds. Sonic and Knuckles walk off to try and come up with a plan, but Tails' cry of help is quickly stifled. The two heroes spin around to see that Tails is being crushed by the crystal Robotnik! Knuckles charges in to end things quickly but is knocked out by Robotnik's new eye-beam. Sonic tries a Spin Attack but Robotnik resists by turning himself into a giant. As Sonic begins to dodge the laser blasts, Robotnik explains that he was never dead, his body just took some time to adjust to the Emerald power he'd absorbed. Sonic wishes he'd smashed the Robotnik statue while he had the chance but Robotnik laughs it off, finally hitting Sonic with an attack.
With the heroes scattered across the room, Robotnik declares that he doesn't need Grimer or the Drakon Empire anymore - he is the force! Knuckles wakes up and bursts through a wall, but Robotnik isn't fazed. He's far too interested in killing Sonic, but Knuckles appears from a higher wall and tells Sonic to press "the button" on the control panel next to him. Since there are dozens of buttons on the keyboard, Sonic hurriedly presses all of them. Fortunately, Sonic hits the right one eventually and the Master Emerald blasts Robotnik into nothingness. Knuckles reveals that Robotnik had forgotten about the Chaos Emeralds and now the Master Emerald has absorbed Robotnik's power in a split-second, meaning he's dead! Unfortunately, the gang hear an evil laugh from outside. Robotnik isn't dead - he's now just a giant (non-crystal) God holding the Floating Island in his hands.
The heroes rush out and plan to put a stop to this but Robotnik is convinced he now "rules supreme". To demonstrate his abilities, he hits Sonic with a laser beam and the hedgehog wakes up in a desolate city. Confused, Sonic supposes the logical reason is that Robotnik put him here while he was knocked out. Taking in his surroundings, Sonic notices two citizens being hassled by a Trooper patrol, soldiers that hadn't been seen since RBR. Having a bit of fun for the first time in a while, Sonic easily smashes the Troopers and discovers that the two people being hassled were Amy Rose and Johnny Lightfoot! However, the two people are shocked that Sonic knows their names and Johnny wonders if its one of Robotnik's tricks, the rabbit also wonders if the hedgehog is insane, but Amy plays along, revealing that the desolate Zone they are in is actually the Emerald Hill Zone! Sonic is aghast, saying the Zone should be full of flowers and trees. Amy says it's now used to process radioactive waste. Finally finished with Sonic, the ex-Freedom Fighters are quickly harassed by "Oscar the Pig" and his Death Squad.
Amy and Johnny escape as Oscar questions Sonic. The pig doesn't understand why Sonic is calling him Porker Lewis and checks his database for a "Sonic the Hedgehog". Sonic doesn't seem to exist so Oscar orders his Badniks to take Sonic in for interrogation. Having enough of the situation, Sonic rips into the Troopers and leaves Oscar cowering in fear. Finally, Robotnik makes an appearance and tells Sonic that Porker doesn't know who he is. In fact, Sonic has never existed! Without Sonic, Amy and Johnny never had the courage to become Freedom Fighters. Porker is terrified of Robotnik and has become his most devoted slave. Sonic asks what happened to Tails, and Robotnik is particularly happy about this one. He asks Sonic how he met Tails, the hedgehog replying he pulled him out of a bog in the Swampland Zone. The tyrant cackles, reminding Sonic that since he never existed, nobody was there to pull Tails out of the swamp. Sonic is distraught - that his best friend Miles "Tails" Prower is dead.
Sonic vows to end this madness, but this is how Mobius would look if Sonic had never existed. Robotnik has already won! Sonic says he'll beat him in the end, but Robotnik devises a plan to challenge this. Sonic is sent into the future, where he believes that Robotnik has turned into his normal self (perhaps because of bad eyesight). He attempts a Spin Attack but falls over, out of breath. Robotnik, conjuring up a mirror, tells Sonic he has arthritis, something the old hedgehog has been suffering from for years. The doctor reminds Sonic he said he'd beat him in the end, but 65 years into the future sees the world celebrating 70 years of Robotnik Day. Robotnik revels in the "fact" that Sonic will spend 65 years fighting for nothing. Back in the present, Sonic has returned to normal, so he attempts another attack. Unfortunately, the hedgehog sinks right into Robotnik's body and ends up on a stage. A "Robotnik" disguised man mocks Sonic for being the "worst Sonic" actor they've had on stage, with an audience full of Robotniks booing in agreement. Robotnik continues to alter reality, delving into the world of Peter Pan vs Captain Hook, Road Runner vs Wile E. Coyote, the Houses of Parliament, the ocean (as fish) and a vampire hunter against Dracula (all of them still obviously Sonic and Robotnik).
Back to normal, Robotnik promises to make things easy; if he surrenders, Sonic can become Robotnik's personal slave. The hedgehog laughs it off, knowing he'll win eventually. Without his powers, Sonic could defeat Robotnik in seconds, especially since in the past, Robotnik and other foes haven't even slowed him down. Realising Sonic "yearns" for the good old days, Robotnik comes up with the idea to summon one of Sonic's old villains from the street debris. The answer is for Sonic to fight the original Metallix!
- The story follows on from Order & Chaos, despite the previous adventure being The House on the Hill.
- Sonic pressing all the buttons and only the desired effect happening suggests the other buttons do nothing at all.
- The final panel of the first part has become the most famous butchery of all, the Floating Island being replaced by a chocolate cake about to be eaten by the giant Robotnik.
- Porker's original name of "Oscar" was revealed in On The Run, which ran shortly before this story.
- Without Sonic around there are a few plot-holes and storyline problems
- With Sonic having never existed, there was nobody around to make sure that Doctor Kintobor turned into Robotnik in the accident, a theory is that all Robotnik, just rubs out Sonic and that he's from the alternate timeline with Sonic, another theory, is that there was no need to create Metallix, so Robotnik just remains him.
- Amy is pink, but without Sonic, Amy never would've gotten her pink hue as revealed in Amy's Secret Past.
- With Tails dead without Sonic, it's unknown what happened to the Nameless Zone, it could be assumed that Trogg took the Zone over.
- The meeting with Tails happened in Issue 27, something many readers never read until later.
- The only other story to coincide with the events of Robotnik Reigns Supreme is Show of Strength, where Sonic continues to help out the citizens of the battered Mobius against the reign of Robotnik. Sonic continues his Taking the Plunge story despite also being on the Floating Island.
- The 70th anniversary of Robotnik Day suggests that Robotnik took over 5 years prior to the events of this story... in other words, at the very start of Sonic the Comic. It has been said that the events of the first two Sonic the Hedgehog video games occured before the events of STC so, with no Sonic to stop him, Robotnik could easily have taken over before this.
- Sonic doesn't notice he's turned old, despite having a beard and he's holding a walking stick.
- Sonic also wishes to catch Robotnik off-guard before attacking, but yells at him as he goes to charge. This could perhaps be a sign of senility.
- Many people believed the Houses of Parliament scene to be in a court.