Archie Sonic the Hedgehog Issue 159 was the one hundred and fifty-ninth issue of the main Sonic the Hedgehog comic series.
- "System Reboot"
Sonic and Shadow begin fighting after Shadow blames Hope's injuries on him, and Sonic attempts to persuade Shadow that he's not involved with the Metal Sonic Troopers, with Shadow countering that that resemblance between them implies a connection. Rosie then berates the two hot-heads, reminding them that Hope is injured. Sonic then grabs Hope and rushes her to the castle to receive medical attention, with Shadow in hot pursuit. Elsewhere, Charles berates himself for creating the Metal Sonic Troopers in the first place, as they have gone from being potential defenders to attackers. Rotor comforts him in his misery, and reminds him that "it's not the invention that causes the problem, but the purpose for which the operator utilizes it." Back in New Megaopolis, Eggman is fascinated as the Metal Sonic Troopers 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 as the Chaotix battle Metal Sonic Troopers, and a determined Shadow somehow causes Chaos Control to create a portal for them. Knuckles is astounded, recognizing the energy, while time warps to bring the duo of Hedgehogs to the castle five minutes previously. The two then turn Hope over to Doctor Quack, while Sonic confronts Elias about the Metal Sonic Trooper project. The two then decide to put aside any argument to deal with the Troopers, and Sonic speeds off to battle. He confronts the Troopers, who accuse him of threatening the kingdom, but are then caught up in a cyclone that Sonic sets off with his speed. Unfortunately, they are able to escape and attack him again, only for Shadow to arrive on the scene and leap to Sonic's aid. He is then astonished as the Metal Sonic Troopers are defeated simply by the raise of his hand, while Knuckles arrives and remarks that Shadow must have used Chaos Control by drawing powers 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 then proposes a party to celebrate their victory. Elsewhere, Shadow contemplates Sonic's farewell to him, while Uncle Chuck observes him on a monitor.
- "The Despicable Dr. Robotnik: "Insidious"
A.D.A.M. greets Robotnik as he enters his control room, though Robotnik is less than happy. A.D.A.M. remarks that his research is going forward and the empire is being held together well by his lieutenants, though Robotnik replies that his underlings are all "sniveling worms looking to stab me in the back at the first chance." He expresses his anger over Snively's defection to the Freedom Fighters, when A.D.A.M. proposes that an example be made to ensure the loyalty of his other lieutenants. Robotnik laments that Snively is beyond his reach, but A.D.A.M. then reminds him of the recent release of the nanites. A.D.A.M. then reports that the Freedom Fighters took several nanites for study, infuriating Robotnik until A.D.A.M. reveals that he is still in contact with the captured nanites, including those fused to Tommy Turtle's shell. He then taps into those same nanites, revealing a room where Jules and Charles Hedgehog are awaiting Tommy. Then then have Tommy put his hand down on s scanner and look into a camera in order to set up their new security system, which A.D.A.M. takes advantage of by triggering a growth spurt in the nanites. They infiltrate the security console, and Robotnik is delighted to realize that he can manipulate the nanites in the heart of enemy territory. Jules and Bunnie Rabbot are next in line, and are infiltrated by the nanites, though Robontik briefly worries that they might be depleting their supply of nanites. A.D.A.M. assures him that the console is providing the nanites all needed sustenance, but Robotnik then becomes worried as the infiltrated Bunnie starts looking woozy. Fortunately for the villain, Bunnie waves it off, and he anticipates Sonic's participation—until A.D.A.M. reminds him that Sonic is fully organic and thus immune. Robotnik questions how Tommy was infiltrated, and A.D.A.M. replies that the shell's composition is compatible with the nanites. He then points out that NICOLE would be susceptible, and has his nanites infect her, leaving Robotnik to gloat over his new secret weapons.
- Sonic: Ready to call it a day?
- Shadow: I haven't even started, hedgehog!
- Hope is taken to the castle to receive medical treatment.
- Shadow learns from Knuckles that he possesses the ability to draw directly on the Chaos Force.
- The Metal Sonic Troopers are defeated.
- A.D.A.M. places nanites in Bunnie, Jules Hedgehog, Tommy Turtle and NICOLE.
- This is Ken Penders' last issue as a main writer, though not his last published story.
- This is Ron Lim's last issue as penciller.
- The small wind-up toy on the cover resembles Metal Sonic Kai from the Knuckles Chaotix special.