Deep within Angel Island, Knuckles the Echidna is invading a hidden underground temple. He confronts an unavoidable series of booby traps, but manages to evade every one of them, despite setting off every trap. Brushing himself off after a close call, Knuckles begins to muse about how he got here.
He recalls how someone named Archimedes captured the Chaotix. Archimedes plagued the echidna with taunts riddles, causing Knuckles to begin a quest to find his friends. His search for answers led him to Mount Fate. Knuckles also recollects Edmund and Dimitri's endeavor to return the island to Mobius, only to have the latter become power hungry, absorb the powers of eleven Chaos Emeralds, and be buried under his own ruins. Knuckles concludes that Mount Fate, his current location, is most likely where his friends are being held.
Suddenly, the echidna activates another trap, sending a gigantic boulder rolling his way. He manages to outrun the danger and escape through a doorway too small for the boulder to fit through. However, he encounters a corridor full of metal doors. As Knuckles finds a portable concussive blaster behind one door and blows an entrance in another, a figure surfaces from beneath Mount Fate. Skulking down the newly discovered hallway, he trails an unknown, taunting voice. He finds the source of the voice: Archimedes, and his friends dining in good condition. Meanwhile, the mysterious figure looms through the bowels of Angel Island.
A bemused Knuckles recounts previous events in his search for the Chaotix, including Archimedes' ability to vanish into thin air and carve his name into solid granite. Archimedes slightly toys with the rejoined Chaotix by vanishing and spewing fire at the team. Although Knuckles is unimpressed by the fire ant, Archimedes counters by saying how his people saved the echidnas back in his day.
The being that was tailing Knuckles confronts the Chaotix, revealing himself to be Dimitri, transformed into Enerjak. Knuckles refuses to believe Enerjak's identity, stating that Dimitri died in the ruins of his dark tower. Enerjak informs that the power of the eleven crushed Chaos Emeralds made him immortal, eternal, and indestructible. The Chaotix charge in, but Enerjak easily paralyzes the team. Enerjak declares his plan for conquest, and notes that he could "use" the Chaotix to his advantage. He then proceeds to teleport Knuckles and Archimedes, thinking they deserved a "better" fate. The two find themselves in the Sandopolis Zone.