Knuckles the Echidna reflects on the friends, family, and enemies he's recently gained while Enerjak spins him around near the surface of one of Mobius's moons. Enerjak promises that Knuckles will pay for what he and his forebearers have done and gloats about his limitless power. Knuckles reminds him that he was defeated in their last encounter. Enerjak teleports Knuckles to the depths of the ocean, hoping that he'll eventually understand that he is doomed and relent.
Meanwhile, Julie-Su arrives at the Dark Legion camp and is questioned about her recent activities by Kragok. She explains that she was with the Guardian, using him to find a way back to the Legion, but ended up whisked back to the camp by Enerjak himself. Kragok accepts her report, but warns her not to push her luck. Julie-Su explores the base, feeling a bit distant with her former comrades, and reports to her Sergeant, Rykor. Meanwhile, Lara-Le meets with Constable Remington and asks him to allow her to speak with her ex-husband, Locke. Remington thinks back to the teachings of his predecessor, Holmes, who warned him about being personally involved with the Guardians and their affairs.
Deep under the sea, Knuckles refuses to give in to Enerjak's will and swims back towards the surface. He manages to elude a shark and
nearly make it to the surface, but is grabbed by a horrible sea monster while Enerjak gleefully watches Knuckles squirm. In Haven, Locke wakes up from his journey into the mind of Hawking. Sabre tells him that Hawking remains in his coma when the facility's alarm goes off. They rush to their spy cameras and find the Dark Legion preparing to strike Echidnaopolis, with Julie-Su among their ranks. Meanwhile, Knuckles manages to escape from the sea monster's hold and reaches the surface. Enerjak demands that he beg for mercy, but Knuckles refuses once more.
At the Dark Legion camp; Espio, Mighty and Vector are being held hostage when they spot Julie-Su nearby. Vector loudly
complains about Julie-Su being a turncoat, which grabs the attention of a Legionnaire. While the Legionnaire tries to tell the group to quiet down, Vector knocks them out and steals their gun. Julie-Su sprays the Chaotix with knockout gas. Kragok applauds her quick action and orders her to finish them off. Meanwhile, Knuckles is teleported into the stratosphere and flung towards the surface of Mobius. Back at the camp, Archimedes and Deo Volente are placed in a mechanical plastic cooler and buried alive. The cooler emits a strong electromagnetic field, preventing them from teleporting out.
Knuckles nearly lands headfirst on jagged rocks when Enerjak stops his descent, demanding that he surrender. Knuckles blows him a raspberry. Enerjak is so upset by this disrespectful tongue blowing that he decides to take Knuckles apart literally, tearing his atoms away one by one.
This issue's cover is the second part of a three-part image.
While tearing Knuckles apart atom by atom, Enerjak tells him to "enjoy life as a neuron". As he is reducing Knuckles to subatomic particles, he was most likely meant to say "neutron".