Having been banished to the Sandopolis Zone by Enerjak, Knuckles and Archimedes start making their way out of the desert, only to be attacked by a giant Sandcrawler, larger than any Knuckles has ever seen. After hearing Knuckles observe that Sandcrawlers track their prey by their body heat, Archimedes draws the beast's attention with a blast of his fire breath and leads the creature towards a rock. The Sandcrawler strikes the rock and is instantly killed. The pair cook the fallen carnivore, before Knuckles asks Archimedes to explain his comment that fire ants had "pulled echidna fat out of the fire" as far back as the origin of Floating Island.
Archimedes explains that the Fire Ants have been present on what is now the Floating Island for many of the major events of its history, including its being lifted from the continent of Downunda using Chaos Emeralds. Unbeknownst to the Echidnas, the Ants aided them in this endeavor by using their super strong mandibles to chew away the rock binding the island to the surface, allowing the island to escape the White Comet. After noting that this was but one of many instances of the Ants stepping in to assist the Echidnas, Archimedes recites the incident surrounding Dimitri's transformation into Enerjak, and how the Ants ate the foundations of his fortress in order to bring it down upon him, creating Mount Fate and seemingly burying him forever.
Archimedes ends by revealing that ever since Enerjak's initial defeat, the Fire Ants have continued to assist the Echidnas ever since. Archimedes' previous encounters with Knuckles have been tests to determine his readiness to deal with future tasks. Realizing that Enerjak has had centuries to plan his revenge, Knuckles determines that they must make their way back to the Grand Conservatory before those plans are set into motion. Unbeknownst to the pair, Enerjak has already made his way to the former site of Echidnaopolis, where he uses Chaos Force to raise his new capital of Nekronopolis.
Back in Sandopolis, the desert heat takes a toll on Knuckles, who longs for water and food. He pops his companion into his mouth, but Archimedes escapes using his fire breath. After Archimedes berates his companion, the two press on, but Knuckles is nearly overcome by the desert heart. Just as Knuckles is about to give in, a vision of Knuckles' father Locke appears, offering his son encouragement. The beleaguered pair follow the vision, which leads them to an unexpected oasis in the desert. After recuperating and gathering some supplies, the two continue their trek. They briefly ponder the mysterious circumstance, only to notice the completed Nekronopolis ahead of them. Suddenly, the oasis disappears, leaving them bewildered.
The pair make their way to Enerjak's citadel. After attacking several guards at the entrance, they bring the entire army down on them–just according to Knuckles' plan. The pair infiltrate the citadel, closing the main gate behind them and destroying several more Mechanauts. As they make their way deeper into the fortress, Knuckles notes with some suspicion that they have met very little resistance. His fears are confirmed as he is tripped by an unseen assailant, stung on the head, hit with a sonic blast, and struck by a super-strong punch. Knuckles gets to his feet as his assailants–Espio, Charmy, Vector, and Mighty–reveal themselves, and Knuckles realizes that he must defeat the brainwashed Chaotix if he is to reach Enerjak.