The story arc starts out in Sonic The Hedgehog #180, where the former Enerjak, Dimitri the Echidna, tells the newly established Acorn Council about his time as Enerjak, how that when he tried absorb the power of Chaos Emeralds, the energies made him a demi-god. He also said that he was intend to be Enejak with the help of Finitevus, but the mad docotr pulled a double cross and now everyone is in trouble; all the while Sonic tries to ask Eggman for the help with the new Enerjak.
Knuckles crossing over
In issue 181,Sonic and Tails take he Tornado to Angel Island, where NICOLE's spy-bots watch the new Enerjak taking sending the Dingoes Army to the Island's desert, Sandopolis, and destroying General Kageby tearing apart at the atomic level. But the Blue Blur arrives too late as Enerjak transports the civilian echidnas, which includes Knuckles's mom, step-dad, and baby half-borther; and then takes the Dark Legion's cyborg implants, declaring that his mission is to destroy all of technology. By the time Sonic reaches the power mad echdina, Enerjak teleports himself to the nanite-form city of New Mobotropolis, where he reaveal to the Chaotix and Freedom Fightersthe echidna behind the mask is none other than Knuckles! In a back-up story in the issue, it goes into detail about how Knuckles became Enerjak. Fintitvevus manage to capture the Guardian with the help of the Destructix and took him to the Shrine of the Master Emerald. He tempted Knuckles with idea of using the Master Emerald's power in order to save last 10% of the echidna population since General Kage's take over. But what the guardian didn't know was that Finitevus had put negative-energy in the Emerald, allowing him to mold the new Enerjak's mind into doing one thing: Destroy all technology of Mobius!
In issue 182, Enerjak declares that he'll free the people of New Mobotropolis of the evils of technology, but Sally opposes from his rampage on Angel Island, NICOLE defends tech by stating how it gave her a chance at life, and Julie-Su begged Knuckles to stop from his past deeds with the Chaos Powers . Of course, Enerjak was not pleased.
As Enerjak was about to 'liberate' Julie-Su from her cybernetic implants, Sonic dives in and save her. As Sonic charges Enerjak, ignoring Sally's warnings about who Enerjak is, Shadow shows up as reinforcement from Guardian Units of Nations. As fast and powerful as the hedgehogs are, they are hardly a match for living the god. As Enerjak attacked Sahdow, Sonic knocks off the echdina's helmet and fond out that he was fighting his main man Knuckles! Not willing to fight, the Sally rallies the Freedom Fighters, Choatix and the civilians to charge Knuckles, only to be frozen still. All hope seems lost until Dr. Robotnik and his Eggfleet appeared and transport Knuckles to Eggman's Egg-Grape vineyard. Shortly after, Sonic and Sally arguing over if they shold escue Knuckles or not when a warp ring appears and someone's arm grabs and pulls both Sonic and Julie-Su through. It turns out to Knuckles's father, Locke. He proses a plan to stop Enerjak, by destroying him! In the back up story, it tells us about Dr. Finievus's origin and his reign of terror on the echidna population.
In Issue 183, Julie-Su and Locke agrue over that they should save Knuckles or destroy him. This is around when the Destructix showed up, sent by Dr. Finievus to stop's Locke's plan.
Meanwhile, Eggman tries to drain Knuckles' energies in the egg-grapes; but power proves too much and overloads Eggman's entire base.
Back on Angel Island, Sonic, Juie-Su, and Locke were fighting the Destructix and were loosing ground until
Archimedes appeared and used a firewall to buy the heroes some time to get the weapon, even though he shows that he doesn't think of destroying Knuckles is the right think to do. While the two argue and after the Destructix show up, Sonic got the weapon, only to destroy it. Witht the weapon gone, the Destructix fall back. Locke is outrage by the fact that Sonic destroyed the only chance to stop Enerjak, Sonic points out that he came up with his own plan, and races out of the temple.
After destroy what's left of Eggman's troopsa and war ships, Knuckles has drain most of his energy. He then teleports back to the Master Emerald where Dr. Finievus was hiding and ready to give the echidna another power boost until Sonic comes in and interrupts Finievus's chant and lands on the Master Emerald. Sonic then recalls how Anti-Sonic became Scourge and how he beat Perfect Chaos. In other words: Sonic uses the Master emerlad to become Super Sonic and to beat the evil out of Knuckles.
Issue 184 opens up with everyone in Albion and New Mobotropolis watching Angel Island as Super Sonic and Enerjak blasting off into the sky and battle. Sonic taunts at Enerjak's attempt to destroy him. Back on Angel Island, Locke mumbles to himself how Sonic stop his attempt to stop Enerjak, but Julie-Su snaps at him about how easily he was going to destroy Knuckles, even Archimedes was against him. Else where on the Island, the Destructix fall back now that Finitevus has what he needs; all except for Fiona and Scourge, who then leave through a Wrap Ring.
Back at the fight, Super Sonic notices that cleaning Knuckles aura is taking longer than with Perfect Chaos. Meanwhile, Julie-Su faces Finitevus, threating him to stop what he was doing
, the doctor replied that he can't. The Hex that he put on the Master Emerald, which bent Knuckle's intentions to his own,can only be broken when some gave their life. This hardly phased Julie-Su, she wouldn't want Knuckles to live this way. Archimedes states that he should do it, he was Knuckle's teacher and that Julie-Su has her life ahead of her. But then Locke
appeared from a Warp Ring and say' he'll do it, he wants Knuckles to be safe. Finitevus attacks to stop them, ranting that the world needs to be cleanse
by fire. Archimedes then grabbedechidna doctor and teleported away. taking this time window, Locke boldly climb the stairs to the Master Emerald, giving Julie-Su some last words, sat upon the Emerald, and started chanting while Sonic and Knuckles continue to
battle overhead. And with his last words, Knuckles turn back to normal
After Sonic safely lowers Kuckles back onto Angel Island, Julie-Su rushed up to him and hugged him with tears, telling Knuckles about Locke's fate. At this time, Finitevus has cme back from a Wrap Ring, ranting about his foiled plans. Knuckles immediately charges at him, remembering everything he has done. He puches the doctor over the edge of the Island. When Knuckles wants more of punching Finitevus, but the vile doctor manges to escape through a Warp Ring.
With the whole ordeal over, Sonic and Julie-Su offer Knuckles to go to New Mobotropolis, to let all his friends show that his back to normal, but refuse.Knuckles states that he the of the Guardians, and that it's his duty to protect the Island and the Master Emerald... alone if he had too.