Just as the Rebellion has gotten used to peace since the Chaos Council had unexpectedly left New Yoke City, they find their ship returning with additional Prism Shards. Anticipating how bad things will get, they and Sonic team up once more for a direct assault on their headquarters. The Council itself makes plans to harness the Shards' power and eliminate their enemies for good.
- Big "NO!": Rebel lets one out when the Chaos Council return and reactivate New Yoke City's defences.
- Can't Kill You, Still Need You: While the rest of the Chaos Council insist that Nine has outlived his usefulness, Mr. Dr. Eggman interrogates him into finding a way to beat Sonic. He then uses him as bait for Sonic while he creates a weapon to finally take the hedgehog down.
- Chronic Hero Syndrome: Sonic insists that taking back the Prism Shards is the key to help the rebels, but his instincts draw him to battle in order to help them.
- Cliffhanger: As Sonic, Rebel, and Knucks make their way to the Yoke, they face a robot that resembles Sonic himself.
- Evil Cannot Comprehend Good: Discussed when Nine tells Mr. Dr. Eggman that this is one of the reasons the Chaos Council will never defeat Sonic: they don't understand how his mind works and can't think like him. This backfires, as it gives Eggman the idea to create a robot that can think like Sonic.
- Forced to Watch: Attempted when Mr. Dr. Eggman forces Nine to watch as Dr. Done-It's Jumbo Eggforcers attack Sonic and his friends. Of course, the Jumbo Eggforcers lose.
- From Bad to Worse: The Rebellion has their work cut out for them after the Council's return. The Council resumes their attack against the Rebellion. They soon use the Shards to upgrade their robots, and even create a new one with the same likeness and power as Sonic.
- My God, What Have I Done?: Eggman demands Nine to tell him how to beat Sonic. Nine tells him that Sonic is too fast to be stopped and too determined to defeat, not to mention no one in the Council has even thought of thinking like Sonic. Eggman believes that last part is the key, and Nine realizes that he just played right into the Doctor's hands.
- Nice Job Breaking It, Hero: Nine's impassioned defence of Sonic ends up giving Mr. Dr. Eggman an idea for how to defeat Sonic, and his panicked attempt to relay this to Sonic gets him caught in the act by Dr. Don't, exposing him as The Mole.
- Taking You with Me: One of the Chaos Council's drones grabs a Resistance member and flies in front of an incoming train, intending for them both to be destroyed. Sonic is able to rescue the Resistance member in time.
- Tempting Fate: Rebel and Knucks are seen discussing how, with the Chaos Council gone, they can finally restore New Yoke City to what it was before... only for Knucks to be cut off mid-sentence by the Council's return.
- Wham Shot: Chaos Sonic's intro at the end.
- When All You Have Is a Hammer…: While the previous episodes implied it, this episode hammers it home: even with the reality-warping powers of the Shards at their fingertips, the Chaos Council are completely incapable of coming up with a strategy to fight Sonic that isn't just "sic wave after wave of Eggforcers on him". Mr. Dr. Eggman is at least smart enough to realise that they need to try something else, but even he can't think of anything until Nine accidentally gives him an idea.
