A ruthless army of technologically-enhanced echidnas named the Dark Legion escape from the Twilight Zone after their banishment from Mobius Prime by Steppenwolf, the founder of the Brotherhood of Guardians. They instantly begin wreaking havoc on the Floating Island, which alarms Knuckles, who doesn't know much about the history of the Dark Legion, and the fire ant Archimedes. With the help of the Chaotix, Knuckles and Archimedes attempt to stop the invasion, but they are soon outnumbered and taken by the Dark Legion as prisoners. After being cornered by the invading forces, the leader of the Dark Legion, Kragok, reveals himself as an echidna with a cybernetic implant on his eye, much to Knuckles' surprise, who believed he was the last of his kind.
The history of the formation of the Dark Legion is shown hundreds of years prior to the storyline. Two echidna scientists, the brothers Edmund and Dimitri, present their idea of returning the Floating Island to the Mobian surface to the Echidna High Council. Though many believed the council would accept their idea, it was denied, angering Dimitri, who declares revenge on the council. In addition to that, the High Council declared that all technology was dangerous, and should be removed from Echidnapolis. Dimitri attempted to use the brothers' invention, the Chaos Syphon to retaliate against the council, but to no prevail. Instead, the power of the 11 Chaos Emeralds was transferred into Dimitri himself, transforming him into the Enerjak, an extremely powerful, god-like being. However, his tower, Mount Fate, crumbled on top of him thanks to the fire ants, supposedly killing him. Dimitri's son, Menniker, vowed to avenge his father by carrying out his ideals. Several years later, Menniker and Steppenwolf, Edmund's son, work to rid Echidnapolis of technology, thought Menniker still keeps technology and thinks it absurd to rid the advanced race of Echidnas of it. He formed a rebellion of hundreds of Echidnas who opposed the no-technology law and supported technology, creating the Dark Legion. Steppenwolf tried to put an end to his cousin's actions by publically retaliating, but is chased down by Dark Legion sentries.
Steppenwolf: Dad! Are you alright?
Menniker: My father! Where's my father?!
Steppenwolf:(to Edmund) I was so worried about you!
Echidna Scientist: (to Menniker) No lad! You can't go in there!
Menniker:(to Echidna Scientist) But my father...
(Mount Fate collapses)
Edmund:(to Menniker) I'm very sorry, Menniker, but your father....Come boys, let's go home.