The story starts with the Chaotix relaxing and waiting for Knuckles to contact them. Suddenly, a shockwave rocks the Floating Island and they are wondering if Knuckles knows what it is. Meanwhile, Knuckles is teleported by Archimedes into Echidna Towers, where the dingoes are holding Lara-Le and Wynmacher. They notice Knuckles' appearance to which he begins attacking the dingoes in the room. Wynmacher helps Knuckles take down the remaining Dingoes and Lara-Le is happy to be reunited with Knuckles. Archimedes interrupts them that more dingoes heading towards them. Meanwhile; Remington, Julie-Su and the Echidna Security Team are given orders to head back to base when they notice a disturbance in the streets. Hawking notices another disturbance when Deo Volente appears to him. They are unsure who is truly causing the disturbances and Hawking theorizes that he needs to contact Haven. He manages to get through to Locke in a scrambled message who tells him that the disturbance originated in Robotropolis. He reminds him of the signs of the zone collapse being when the Dark Legion invaded the Floating Island and when shockwaves happened in the Marble Zone. They conclude that the echidnas and the dingoes are going to be on a collision course for the same space in Echidnaopolis and only one will survive.
Back at Echidnaopolis, Remington escorts Lara-Le, Wynmacher, Julie-Su and Knuckles back to their base. Remington decides that they need to regroup to fight back against the dingoes and rescue the others. Knuckles, Lara-Le, Wynmacher and Julie-Su wait in his office as Lara-Le explains the situation with his upbringing. Remington appears receiving word from Guardian Hawking when another shockwave sends the echidnas and dingoes in the same city and back again. In Cavem Canus , General Von Stryker orders to pull a final act before the zone collapse. A group of dingoes are about to shoot down the captured group of echidnas when Knuckles and Julie-Su appear and attack them. They take them out and Knuckles tries to get information out of one of the dingoes, but is unable to. The captured echidnas lead them towards General Von Stryker when another shockwave occurs. Archimedes tries to get Knuckles to evacuate with the other citizens, but Julie-Su convinces Knuckles that they need to go after Helmut. In his headquarters, Gerbil is panicking from the shockwaves, but General Von Stryker prepares for the shockwave by putting on his power glove. Knuckles and the others arrive and Knuckles tries to convince the general to get to cover. The general begins fighting Knuckles while the echidnas and dingoes head out of the building to safety except Julie-Su. During the fight, Julie-Su covers General Von Stryker with a curtain and Knuckles succeeds in stunning the general.
Knuckles manages to convince Helmut to call a truce for now and they rush to the bunker under the building. The echidnas and dingoes lock up the bunker and Helmut, Knuckles and Julie-su are teleported through by Archimedes. The shockwave causes the group to appear in front of the other echidnas and Remington. They all emerge from the bunker with Echidnaopolis still standing and realise they are on the Floating Island. Archimedes meets up with Deo Volente and leads Knuckles to something Hawking wanted to give to someone special.Knuckles doesn't believe him but Deo Volente gives him Hawking's hat that he will understand what makes him special someday. Deo Volente teleports away and Knuckles admires his hat to Archimedes approval.