Continuing from the last issue, Knuckles finds himself facing off against the brainwashed members of the Chaotix, who warn him that Enerjak will prevail regardless of whether he chooses to surrender or fight. Archimedes whispers a warning to Knuckles, before unleashing a fire blast as he and Knuckles engage their manipulated allies. Vector quickly pulls out a fire hose to counter, only for a bank of fog to rise up. The confused Chaotix then hear a strange echoing voice, only for the source to be revealed as Knuckles and Archimedes reappear and attack. Knuckles lands blows on Mighty and Vector, and Archimedes hits Charmy with his fire breath, but unbeknownst to them Enerjak is watching their battle. Recognizing that his brainwashed minions cannot overcome foes with free will, he intervenes, using his powers to knock Knuckles and Archimedes unconscious by cutting off their air supply. He then orders the Chaotix to bring their defeated foes to him, while musing on the events that have led up to this moment, from the creation of the Floating Island to his own escape from Mount Fate.
Knuckles and Archimedes then appear in Enerjak's chamber, where he remarks that they were the biggest threat to his plan, which is why he had exiled them previously. He expresses his surprise at their survival, while Knuckles arrogantly retorts that he's really only imagining their presence. To himself, Knuckles muses that Enerjak is unaware of the oasis he and Archimedes found, only to be thrown to the ground by an irate Enerjak. He boasts of his limitless power, which has the capability to hold the island aloft and to create structures like Nekronopolis from the earth, and remarks that he doubts his city will collapse as his Dark Tower did previously. Knuckles expresses doubts about that, signalling Archimedes to contact his Fire Ant brethren, who march on Enerjak's Citadel.
Enerjak strikes with his Chaos Force-based powers yet again, declaring the blow but a sample of what he is capable of doing. He warns the pair that they should be afraid, which they respond to by teleporting out of the room via Archimedes' abilities. Enraged, Enerjak alerts the Chaotix, who leave a card game behind in order to obey their master. They end up rushing right by where Knuckles and Archimedes are hiding, courtesy of one of the Fire Ant's illusions. Archimedes then proposes a counterattack against Enerjak, though Knuckles expresses doubts given Enerjak's ability to strike at them without being physically present. His companion then points out that his illusion has apparently concealed them from Enerjak as well, and teleports the pair into an air vent just above Enerjak's chamber. Knuckles then dislodges a grating and rides it to land on top of Enerjak, who throws him off in a rage.
As the Fire Ants swarm over Enerjak's citadel, Enerjak mocks Knuckles' attack, only for Knuckles to reveal his name and his knowledge of Enerjak's true identity: that of his distant uncle Dimitri. His accusation that Enerjak is the reason for his current status in life is refuted by Enerjak's claims that his brother Edmund is responsible, along with the members of the Echidnaopolis High Council. Boasting that they lacked his courage, he is accused by Knuckles of fighting with enhanced strength, only to claim that he can defeat Knuckles without it. Knuckles then questions his fighting abilities, only for Enerjak to display superior skill. However, in the course of their battle, rocket jets have been mysteriously attached to the upper levels of the citadel, and ignite, carrying the building up through the atmosphere. Knuckles breaks away from the battle, and a piece of the floor breaks away beneath him, while Enerjak is carried into space with his fortress.
Calling Archimedes by a new nickname, Archy, Knuckles goes into a glide, safely descending to the surface of the island. There they meet the Fire Ants, whom Archy thanks, only for them to reveal that they only created an escape route for him and Knuckles, and had nothing to do with the rocket engines. Before they can think long on who might have planted them, they are distracted by Nekronopolis vanishing into thin air-the result of Enerjak's power being removed-and the appearance of the Chaotix, now freed from their brainwashing. When his friends question how he managed to succeed, Knuckles admits that it was only as he learned from his father's lessons, Archimedes, and even Enerjak that he was able to succeed. He acknowledges that he couldn't have defeated Enerjak alone, but managed to do so by relying on others. Enerjak had sensed that he was a loner by nature, but Knuckles had recognized the weaknesses of that and changed tactics, while Enerjak remained wrapped up in the past. Archimedes notes again that Enerjak had no knowledge of the oasis that he and Knuckles found, and that they still have no idea how it came to be or how it disappeared. The Chaotix, however, decide that it isn't worth worrying about, and decide that it's time to celebrate.
Unbeknownst to the heroes, they are being observed by a hooded Echidna in an unknown location, who commends them for their victory. He then reveals that Knuckles' efforts in fighting Enerjak allowed him to plant the rocket engines that carried the citadel-and Enerjak with it-into space. He also notes that Knuckles has learned his lesson from history: "We are all together as one!" He is also pleased by Knuckles' acceptance of Archimedes, noting that though their two races are natural opposites, they have learned to work together. With this relationship continued, the figure resolves to continue his duty of continuing to watch over Knuckles even as his forefathers have done previously, noting that it is the father's duty to watch over his son, thus revealing himself to be Knuckles' father Locke.
Later, Archimedes and Knuckles sit talking together, and Archy admits that he had thought Knuckles incapable of adapting to different circumstances, but that the Echidna had surprised him since their initial encounter. He then admits that he believes Knuckles is worthy of his role as Guardian, and Knuckles returns the compliment and remarks that he feels that they have become friends. Unbeknownst to them, however, as Enerjak's citadel flies away from Mobius, maniacal laughter echoes through the void...