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- This issue's story finishes off the story from Sonic & Knuckles: Mecha Madness
Archie Sonic the Hedgehog Issue 40 was the fortieth issue of the main Sonic the Hedgehog comic series.
- "Court Martial"
Going over the events of last issue and Mecha Madness, Sonic, after being returned back to normal, has been thrown in the Jailhouse by the Freedom Fighters. Sonic in jail is visited by Antoine, who Sonic then accuses that the only reason he's there, is because of Antoine's charges. Antoine is now in charge, because everyone important is rebuilding Knothole. Antoine doesn't believe this and plans to celebrate his coronation as the new Commander. With Antoine's departure, Sonic runs along his cell, yelling that he should be out there helping, instead of being in jail. Outside the Jailhouse, Amy Rose is protesting with a blowhorn. Sally and Rotor watch Amy yelling "FREE MY HERO!", While Sally commented that she just worships Sonic. Rotor reports that King Acorn's disaster plan worked with the back-up units stored underground working fine. Sally almost goes into tears for the fact that she has to court-martial the only boy she really loved. Sally to get a grip on the sitation approaches Amy to stop the protest. Amy believing that she's come to pardon Sonic, Sonic tells her through the bars that it won't happen. Amy in tears when Sally tells her that he's staying in jail. Sonic starts yelling at Sally that he doesn't belong in jail, Sally mentions that no one is above the law. Sally drags Amy away, yelling that they'll settle the matter in court.
The next day, Sonic is in court with Hip and Hop as court judges and Antoine prosecuting. Sonic quickly recognises the kangaroos (STH 6), but they tell him that he won't get any special treatment, and they would banish Sonic if they could decide. Sonic asks who decides, when Princess Sally enters in her royal clothes. Sally orders Bunnie to guard the prisoner, with Sonic saying "that's the thanks I get for saving your life" to Bunnie. Bunnie mentions that Rotor's installed a "hedgehog hunter" that will be attracted to Sonic's unique aura if he tries to escape. Sonic looks into the crowd and realizes that Tails and Rotor aren't helping him at all. Sally starts the trial, with Antoine going mad to prove his case, "badgering" Amy and questioning Tails, Rotor, and Bunnie in a way that made Sonic seem undeniably guilty before bragging that he saw everything. Sally ends his case, but Sonic calls Antoine as a witness, stating that, in the events leading up to his roboticization, Antoine had left his post at the jailhouse, which had allowed Nack to escape, capture him, and deliver him to Robotnik in the first place, and Antoine was too busy planning his coronation party to notice Nack had disappeared. Antoine outbursts himself that it's all true, but Sally states that the trial is about Sonic regardless, with Hip and Hop declaring him guilty.
Sonic angrily manages to shred off his handcuffs, scaring Bunnie a bit. Sally then calms them all down, with Sonic begging for a chance to prove his innocence. Sally delays the sentence for 24 hours, giving Sonic a chance to prove himself innocent. Sally gives Sonic a tracking device, so that they can tell where he is, and with that Sonic runs off to find Nack. In Robotropolis, Dr. Robotnik with Orbinaut spots Sonic on the edge of the Badland mountains. Robotnik is angry that he's alive and healthy, plus that almost all of Robotropolis was destroyed in the battle between Mecha Sonic and Mecha Knuckles. Robotnik plans his revenge with his ultimate weapon, and discovers that Sonic is heading to the Robo Hobo Jungle, in an attempt to find the location of Nack. Sonic is then ambushed in order by Caterkiller, Bat Brain and Motobug. Motobug about to slash Sonic, Sonic kicks Motobug out of the area, but is then ambushed again by Buzzbomber, Crabmeat, Burrobot and Splats. Sonic defeats the Classic Badniks, and gets the location of Nack from the head of Caterkiller, when threatened by Sonic. Sonic then zooms to the Bottom of the Barrel Bar 'n' Grill to get Nack. Sonic is stopped by a gorilla from entering and thrown away. Sonic uses his "figure eight" move on the gorilla, causing him to smash through the building. The rest of the citizens run away, and Sonic has Nack cornered. Nack secretly puts fake hands up, and uses his real hands to shoot Sonic with a gas gun. Nack about to flee and leave Sonic in the midst of the gorilla, instead kidnaps Sonic and rides away on his vehicle.
Nack contacts Dr. Robotnik that he's successfully captured Sonic again. Robotnik wants Nack to head to Robotropolis and he'll get his cash, but Nack doesn't want that after last time. Instead he wants the money sent to him, but Robotnik doubts Nack's capture of Sonic. Sonic regains conscious and knocks Nack out, and notices the rebuilding of Robotropolis. Sonic tells Robotnik that he's sending Nack's vehicle to self-destruct on the city. Robotnik doubts the threatening, but is warned by a SWATbot and an explosion sends Robotnik flying. Miles away in Knothole, Rotor reports to Sally about the explosion in Robotropolis. Sally notices that Sonic is due back, but the tracker isn't working. Sonic enters the building with the tracker, that he used as a gas mask filter and throws Nack on the ground, proving his innocence with Nack's confession. Rotor takes Nack to the Jailhouse, leaving Sally and Sonic alone, where Sally, by way of a sincere and heartfelt apology to Sonic on behalf of herself and the other Freedom Fighters, for the tough ordeal they had put him through, tells him she'd never been so glad to be wrong, and Sonic, surprisingly, assures her he has no hard feelings toward her, Rotor, Antione or even Bunnie (despite her actions toward him in Kangaroo Court). Both are relieved that Sonic is innocent and free, and Sally hopes that everyone has Sonic's attitude. Sally and Sonic then walk out to find Antoine getting ready for his coronation and party.
- Sonic: What I'll be is in your face when this trial is over, Antoine! You're the one who brought these charges against me!
- Antoine: Haven't you already perpetrated enough violence upon us? Now you weel add "assaulting zee new Commander" to the list?
- Sally: I'm afarid not Amy. There are some very SERIOUS charges against Sonic.
- Amy: (sobbing) But...
- Sonic: Tolja... Queen takes Pawn... CHECKMATE!
- Sally: Save your emotional outbursts for court... Nine AM tomorrow!
- Amy Rose: (being dragged away by Sally) I still believe in you, Sonic!
- Sonic: And another thing... The chili dogs here are stale!
- Rotor: I'll put Nack back in the jailhouse, Sally.
- Sally: Thanks, Rotor...and thank you, Sonic. I've never been so glad to be wrong!
- Sonic: No hard feelings, Sal.
- Sonic is wrongly put on trial for willingly subjecting himself under Dr. Robotnik's control via Roboticization, in the last issue.
- Sonic decides that in order to clear his name, he has to find and bring Nack the Weasel to justice.
- Sonic brings Nack to Knothole Village and upon his forced confession of abducting the hedgehog, Sally only too gladly clears Sonic of all treason charges against him.
- The book that Antoine is reading from is entitled "The Perfect Party" by Martha Shrewart, a reference to Martha Stewart.
- Amy Rose has appeared since her original appearance from STH 25.
- Dr. Robotnik mentions his 'ultimate weapon', which would not be featured until Operation: EndGame.
- A pin-up is featured with Sonic fighting with the Classic Badniks.