- Sonic has prevented the Sword of Acorns from falling into Doctor Robotnik's clutches, but now it's in the hands of the notorious Kodos, Mobotropolis' former warlord. As if the situation wasn't bad enough, when some unexpected visitors arrive at Doctor Robotnik's doorstep asking for aid, it's up to Sonic to talk them out of such a hasty decision. But why aren't they willing to listen to him?
- Knuckles is on the loose and more dangerous than ever. His fellow echidnas sic none other than the Weasel siblings Nack and Nic on his trail to bring him back. Could there be a showdown in Sonic's feature?
The comic begins with Rotor climbing up a mountain in the Forbidden Zone, attempting to find a way home. As he reaches the top, he is startled as he sees two "meteorites" falling from the sky and he ducks as they land ahead of him. He gets over the cliff to see that if it hadn't been for the energy-dome, they would have struck Robotropolis. He tells himself that although the city isn't Mobian friendly, he needs to check out the crash site. At first he has trouble seeing through the smoke, but then he hears a voice calling for Sonic. Out of the smoke comes Mina Mongoose, who is looking for Sonic. Rotor explains that he's a friend of his. After Mina tells him she thinks Sonic might be there, he drills up to the surface from underground.
Sonic is thrilled to see that Rotor is back, but Mina is angered as she says two giant things fell from the sky, and she wonders how he even survived. Sonic explains that he saw them coming and simply burrowed underground to safety.
At Dr. Robotnik's base, Robotnik is examining the Sword of Acorns, talking to himself about how he thought the meteorites had killed Sonic. He plans to take down the energy-dome and see if the Sword of Acorns can actually restore Mobian free will, as a robotic Uncle Chuck and Muttski enter the room. He prepares to strike Uncle Chuck down with the Sword, but then he throws it away, saying it's ungratifying if he isn't there to see him do it, and leaves.
Back at Knothole, Elias has been alerted that the Sword of Acorns is missing, and he is having difficulty believing that the Secret Service wouldn't have noticed someone enter and leave. He wonders if this could be the work of thieves, but Geoffrey shoots this down because the Sword is the only thing missing, and the person had come especially for it.
At the Knothole Medical Center, Sally is thinking to herself that her whole family had been reunited, only to find out that her father is paralyzed from the waist down.
Nate Morgan comes in looking for Max, saying he came as soon as he heard what happened, and that he should never have gone into battle. Dr. Quack says that it's a bit too late for that, and he says that maybe Nate should accompany the Queen and Sally outside and let the King rest.
Meanwhile, Rotor is saying it's similar to old times - them versus Robotnik - but Sonic says that it isn't the same Robotnik; this one is from another zone and is ten times as evil. He grimaces as he tells Rotor and Mina to get back to Knothole, and when Mina asks him what he would do, he explains how he lost the Sword of Acorns to Robotnik, and now he needs to get it back.
Back in Robotnik's base, Uma Arachnis had just stolen the Sword of Acorns when Uncle Chuck breaks the silence and reveals that he and Muttski have actually reclaimed their free will, but they couldn't have fought Arachnis, or it would attract too much attention. He says it would be better if she had it, or else Robotnik might have found out that it gives Robians free will. He watches the screen where Sonic is fighting SWATbots, just as Robotnik is returning. Robotnik rants about Sonic not knowing when he's beat when he discovers the Sword is missing. He tells himself not to get upset because he doubts it even worked. He then turns to Uncle Chuck and Muttski, saying to himself that he'll let Sonic fight for a lost cause, but he won't compromise the Shadow-bots.
Back at Knothole, Queen Alicia is talking to Nate and Sally, when Nate excuses himself, saying that she and the princess have some catching up to do. The Queen asks Sally what's wrong, and she talks about her father's situation. She's worried about how Elias is doing with the missing sword business. Queen Alicia says she's certain he's doing fine and that he was born for it, and this makes Sally think "...yes, but definitely not bred."
Outside of Knothole, Rotor and Mina are just returning. Rotor finds out that everyone relocated after Robotnik invaded, and asks if Mina is a new Freedom Fighter, to which a stunned Mina says she's just a babysitter. Rotor then begins to ask why she was with Sonic when Elias and Geoffrey see Rotor and greet him.
Beneath the streets of Robotropolis, Arachnis knocks on a door, where a dark figure asks if she has the Sword. She replies that it was a stupid question; of course she did. The figure takes it from her, revealing himself to be Kodos.
On the surface, Sonic hears laughter and wonders where it's coming from, when Robotnik announces through loudspeakers that he is sending Robians after him. Sonic escapes while Uncle Chuck thinks to himself that someone has to keep an eye on Robotnik.
Sonic is racing past the meteorites when he realizes that they aren't meteorites at all; they're aircraft. The doors open up and Sonic says "Now THIS I don't believe."