Sins of the Fathers
- Writer: Ken Penders and Kent Taylor
- Pencils: Manny Galan
- Inks: Andrew Pepoy
- Colors: Karl Bollers
- Letters: Jeff Powell
- Editor: J. Freddy Gabrie
- Managing editor: Victor Gorelick
- Editor-in-chief: Richard Goldwater
- For convenience, this story is summarized in chronological order.
In the distant past, Christopheles the Fire Ant informs the Fire Ant Council that unrest amongst the echidnas continues to grow and the echidna selected to act as a sort of Guardian to his people lacks experience. The queen suggests they send an agent to guide the new protector of the echidnas and Christopheles eagerly volunteers himself. While Edmund reflects on how to inspire the people of Echidnaopolis, Christopheles appears before him and explains that Steppenwolf is in danger due to his meddling. Before Christopheles can give him advice on how to proceed, Edmund rushes on to his mount and heads off to save his son.
Edmund makes his way to the site where Steppenwolf crashed his vehicle, finding two robed cultists searching the scene and managing to gag and knock out one of them. Other cultists notice his presence and shoot him with their laser guns, killing him. The robed men leave and Steppenwolf finds his father's corpse. As he begins to cry, Christopheles appears, offering to help Steppenwolf carry on in his father's stead by training him in combat, the sciences, philosophy, and ethics. After much patience and practice, Christopheles reveals the Chaos Chamber to Steppenwolf and explains that his own energy is channeled through the same power as the Chaos Emerald that keeps the Floating Island aloft. With his training to become the Guardian of the island complete, Christopheles leads Steppenwolf to the Land of the Dark, where he finds his new home: Haven.
In the present, Knuckles and the Chaotix wake up, prisoners at the Dark Legion encampment on the Floating Island. Knuckles is escorted by Legionnaires to the dwellings of Grandmaster Kragok. The Grandmaster greets Knuckles affably and invites him to sit and listen to his proposal, instructing the guards to unshackle him. Knuckles decides to try and strangle Kragok, the guards responding by punching him and smacking him with their rifle stocks until he lets go. Knuckles asks Kragok why he needs his guards to fight for him, prompting Kragok to slap him with his metal arm.
Kragok asks Knuckles where the Chaos Chamber is, but Knuckles refuses to answer. Kragok decides to leave to attend to other business while his guards beat the answer out of Knuckles. The guards are easily defeated by Knuckles, who steals one of their cloaks as a disguise. He heads back to where the Chaotix are being held captive, knocks out the guards, and frees his friends. Knuckles decides that they'll need a distraction, and Charmy suggests they hijack a nearby tank.
Meanwhile, in Haven, Locke watches over Knuckles' progress and begins to discuss the situation with Archimedes when the alarm system goes off. Rushing to find the cause of the security breach, Locke finds his grandfather, Athair. Locke is upset, claiming that everyone is still suffering the consequences of his selfishness, but Athair seems to disagree. The visage of the Ancient Walkers appears behind him and he disappears in a puff of smoke, asking Locke to consider his appearance a warning of things to come. Worried about the message, Locke urges Archimedes to stay by his side so they can try to figure out what they are being warned about.
A few Legionnaires are picking up supplies, ready to move camp to another location on the island, when a tank rolls towards them and a group of Mechanauts and causes a fiery explosion. Kragok and his minions chase Knuckles in their own tanks. Vector is ready to give up running, overcome by exhaustion, when Knuckles asks Mighty to knock over a tree to block the path of the tanks. Kragok sarcastically congratulates Knuckles for his tactical genius and instructs his troops to unload their salvos on the forest, burning it down. As the fire spreads, Knuckles and the Chaotix find themselves in the path of a stampede of Floating Island citizens, fleeing for their lives from the flames.
- This issue's cover is the second part of a three-part image.
- Athair's appearances in this issue were illustrated by Patrick Spaziante, who was not officially credited.
- Edmund is shown riding a Streaking Pasha, but this species' name was not revealed until Knuckles the Echidna #17.
- Although it was previously seen in Sonic the Hedgehog #33, this issue is the first time Haven is addressed by name.
- Edmund's monologue before meeting Christopheles about the citizens of Echidnaopolis being a "cowardly lot", as well as his location (in the foyer of his home, relaxing in a chair, seated next to a large window), is a nod towards the origin story of Batman.
- "N=64" and "32-Bit" are written on Steppenwolf's chalkboard. These are likely references to the Nintendo 64 console and Sega 32X hardware extension.
- Heavy, Bomb, Catweazle, Dylan, Hamlin, and Renfield T. Rodent can be seen in the crowd of citizens fleeing the forest.