Dark Alliance Part Three of Three: Primary Evil
- Writer: Ken Penders
- Pencils: Jim Valentino
- Inks: Harvey Mercadoocasio
- Colors: Frank Gagliardo
- Letters: Vickie Williams
- Editor: J. F. Gabrie
- Managing editor: Victor Gorelick
- Editor-in-chief: Richard Goldwater
At the Master Emerald chamber, Spectre confronts Locke and Archimedes finding them after his search. Both of them argue with Spectre wanting them to help take back Haven, while Locke wants to help Knuckles. Spectre yells that the Dark Legion have taken over Haven, but Locke continues the debate with him. Locke gives in to Spectre and they teleport into the lower levels of the base for the element of surprise. At the Dark Legion's base; Knuckles, Julie-Su and General Von Stryker are captives to Dimitri and Xenin. Knuckles doesn't believe that Dimitri is who he says and tells him that the real Dimitri was going to enslave his own people. He argues that he wanted to continue technocracy in his society, but was unable to and Edmund was used by the High Council to suppress technocracy. He finishes by saying that this is about restoring the echidna society to the way it was.
At his office; Benedict is talking with Remington about their current situation with Pravda standing there like a mindless slave. Benedict tells them that they need change in their society and taunts Remington that he can be replaced, while he will soon have the power of a lifetime. He tells him that Remington should pledge his loyalty to him before that happens. Remington sees him being cocky that he has already declared himself as the winner and Benedict blackmails him that Remington has secrets that could be found out. Benedict sees that his point has been made and begins talking about what he wants him to do. At their base, Knuckles is about to be operated on while Dimitri tells him that he was saved from the aging process by being technologically enhanced. He plans to examine Knuckles to discover his true powers that he possesses. Meanwhile, Xenin is guarding Julie-Su and Stryker while abusing Stryker with hateful dingo humor. In another part of the base, Locke and Spectre take out a pair of Dark Legion troops while sneaking deeper into the base.
Back in Benedict's office, Remington refuses to sell out to Benedict and Remington tries to arrest him. Benedict throws the mindless Pravda at Remington and flees to claim his election victory. Remington rushes after him, but is unable to follow his car. He manages to get a lift via Harry's cab and asks him to follow the car. During the examination of Knuckles, Dimitri believes that Knuckles is a natural source of energy and is able to generate power akin to a Chaos Emerald. Dimitri wonders what would happen if someone would bio-engineer his powers when the alarm goes off. A Dark Legion troop reports that they have tapped into Knuckles' power surges and it is causing their system to collapse. They find their only options left being evacuation or attempting to destroy the source of the problem; being Knuckles. Harry stopped pursuing Benedict when he notices him arriving at his campaign headquarters. Remington decides to sneak in the back and go in solo, since he isn't able to trust his own troops. Through a communication channel, Lien-Da and Moritori Rex give their reports on their situation when they lose power. Both of them try to sneak out through the building when Spectre and Locke confront them. They capture them and send gas canisters through the vent system to stop the other troops in Haven.
At their other base, Dimitri orders his troops to evacuate, seeing that Knuckles is much more valuable alive. Xenin decides to leave Julie-Su and Stryker in their restraints while they evacuate. Benedict arrives into their base and notices an immense electromagnetic pulse discharge being sent through the city. The charge reveals that Benedict is a robot to Remington and Harry. Both of them free Julie-Su and Stryker, but notice the Dark Legion troops injured from the pulse. Harry goes to call the medics, while Remington explores the source of the mess. Remington heads through into the only working room and finds Knuckles exhausted. He realizes that Dimitri is missing and he is revealed to be watching them from a secret location. He narrates that the election ended with Benedict winning, but the position went to the back-up candidate because of Benedict's true identity. Dimitri continues to narrate that Pravda is now forced to spend the rest of his life as a vegetable and that he will have his victory using Knuckles.
J. F. Gabrie is on the phone, telling the receiver that they should do a Sonic/Knuckles miniseries focused on Mammoth Mogul and makes a joke about how he'll work for peanuts. Mammoth Mogul overhears this, angered.
- This issue's cover is the last part of a three-part image.
- The quote attributed to Spectre at the start of the issue is a modified version of a famous statement made during the inauguration of American president Franklin D. Roosevelt.
- On the wall of the alleyway on Page 18, there is graffiti saying "Spaz Rulz" and "JFG" which are the names of the Sonic artist, Patrick Spaziante and the editor, J. F. Gabrie.
- There is also graffiti writing saying "Read" above a drawing of Sonic the Hedgehog indicating a message of wanting readers to read the main series.