- "System Reboot": The action-packed, multi-issue epic comes to a sensational end... and the non-stop thrills are bound to leave your head spinning! As their robotic creations wreck havoc around them, the contrast between the malevolent Dr. Robotnik and the benevolent Uncle Chuck is heightened. Now Sonic, Knuckles and all the good citizens of Knothole Village must restore order from the Metal Sonic Troopers... and you won't believe who their latest ally is! PLUS: The tradition of sizzling Sonic short stories continues with another great back-up tale! Featuring a heart-thumping cover by razzlin' dazzlin' Spaz!
- Writer: Ken Penders
- Artist: Ron Lim
- Inker: Jim Amash
- Letterer: John Workman
- Colorists: Josh & Aimee Ray
- Editor: Mike Pellerito
- Managing editor: Victor Gorelick
- Editor in chief: Richard Goldwater
- Special Thanks to: Robert Leffler and Dyna Lopez at SEGA Licensing
Sonic and Shadow the Hedgehog begin fighting after Shadow blames Sonic for Hope's injuries. Sonic tries to explain that he's not involved with the Metal Sonic Troopers, but Shadow thinks the resemblance is too uncanny to be a coincidence. Rosie halts the fight, admonishing them for their selfish fighting when Hope needs medical attention. Sonic grabs Hope and rushes to Castle Acorn with Shadow trailing none too far behind. Elsewhere, Charles berates himself for creating the Metal Sonic Troopers, which have gone from being potential defenders to attackers. Rotor comforts him in his misery by reminding him that inventions don't cause problems, the people who misuse them do.
In New Megaopolis, Dr. Eggman is fascinated by the destructive potential of the Troopers as they devastate Knothole and is struck by the irony that he must now rely on Sonic to save the day. Back in Knothole, Sonic and Shadow are rushing Hope to the castle while the Chaotixbattle the Troopers. Overcome with emotion as he remembers his failure to save Maria, Shadow reaches out for Hope and creates a portal ahead of them. Knuckles is stunned, recognizing it as Chaos Control. Sonic, Hope, and Shadow arrive at Castle Acorn five minutes in the past, where the Freedom Fighters and Elias Acorn are keeping a lookout over the Troopers. Shadow places Hope in Dr. Quack's care while Sonic confronts Elias about the Metal Sonic Trooper project. They argue briefly before Elias decides to put their differences aside while Sonic deals with the Troopers.
Sonic confronts the Troopers, who accuse him of threatening the kingdom. Sonic points out that the Troopers are destroying the Kingdom of Acorn as they speak, but the Troopers refuse to believe their programming has been compromised. Realizing that facing the Troopers one-on-one won't work, Sonic creates a tornado by spinning around at super speed. It manages to catch a number of the Troopers, but they escape and attack him again. Shadow arrives and leaps to an overwhelmed Sonic's aid. As soon as Shadow raises his hand, the Metal Sonic Troopers are deactivated. Knuckles tells Shadow that he must have instinctively used Chaos Control to stop the robots. Shadow tells him that Chaos Control requires a Chaos Emerald, but Knuckles suggests Shadow drew power directly from the Chaos Force. Sonic, the Chaotix, and Shadow then part ways, and Sonic is welcomed back at the palace and presented a medal of honor and the rank of Gentleman-at-Arms. Jules and Bernie look on proudly, while Sonic proposes they throw a victory party. Elsewhere, Shadow thinks about Sonic's friendly farewell to him while Uncle Chuck observes him leaving Knothole on a security monitor saying they all have their secrets.
A.D.A.M. greets Dr. Eggman as he enters his control room, though Eggman is less than pleasant, furious over Snively's betrayal. He finds himself frustrated that he's unable to exact revenge when A.D.A.M. proposes that he may not be entirely correct about that. A.D.A.M. reminds the doctor of the Nanite City Incident and alerts him to the fact that the Freedom Fighters took several nanite samples for study. Eggman is furious that his technology has been compromised until A.D.A.M. reveals that he is still in contact with the captured nanites, including those fused to Tommy Turtle.
The nanites transmit a live feed of Tommy's surroundings, revealing a room where Jules and Charles Hedgehog are preparing new security measures for the Freedom Fighters. They instruct Tommy to give the computer a hand print and retinal scan. A.D.A.M. takes advantage of this by triggering a growth spurt in the nanites in Tommy's hand, allowing them to infiltrate the security console. Jules and Bunnie Rabbot are next in line and are infected with nanites. Eggman briefly worries that they might be depleting their nanite supply, but A.D.A.M. assures him that the console is providing the nanites enough sustenance to multiply. Eggman is disappointed to learn that the nanites can't bond with Sonic, as they're only able to attach to machines and material like Tommy's shell. They are, however, able to infect NICOLE. Eggman relishes his secret victory, able to spy on the Freedom Fighters whenever he pleases.
- This is the last Sonic the Hedgehog issue to be written by Ken Penders.
- This is Ron Lim's last issue as penciller.
- Ian Flynn was uncredited with touch-ups to the script in this issue, making this his unofficial debut.
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