Air date: January 11, 2004 (JP), January 22, 2005 (US)
As Sonic continues his destruction of the Reflection Towers that power the Sunshine Balls, leaving all of his friends confused by his actions, the President decides he has no choice, and orders the Guardian Units of the Nation to dispatch their Hot Shots to apprehend Sonic. Joined by Topaz and Rouge, they set off, only for Rouge to be distracted by something that caused her to lose some altitude before recovering. It's at this point that she and Topaz discover the transmitter that Eggman is using to control the Egg Moon.
Meanwhile, at the White House in Central City, Eggman reveals that his Sunshine Balls are actually sending out a hidden signal to brainwash the public to garner support for himself.
At the Thorndyke Mansion, wanting to go see Sonic and ask him what he's doing, Amy smashes down a wall for everyone to escape through, only to be blocked by an angry mob led by Jerome Wise that surrounded the mansion. Luckily for them, Sam Speed and the S-Team arrive and force Jerome and the mob to clear out using their status as one of the elite forces of the Station Square Police Department to disperse them under threat of arresting all of them if they laid so much as a hand on his nephew or Sonic's friends, allowing Chris, Amy, and Tails to go find Sonic in the X-Tornado. Meanwhile, Knuckles is convinced by several people to confront Sonic, leading to the two rivals to fight each other before it's broken up by the arrival of the X-Tornado and G.U.N. Hot Shots. With everyone there, Sonic reveals his reasons for destroying the Reflection Towers using a little Astronomy 101 regarding the Earth, Moon, and the Sun, along with their orbits. As everyone realizes that Eggman has tricked them again and is using the Egg Moon to not only make some easy cash but to gain support to become President to enact his latest plan for the Eggman Empire, Topaz relays the info back to the President, who, along with his secretary Christina, are horrified to find they've been played for fools, and with Eggman now in the White House, he's free to take them hostage before making his move to take over the United Federation and the world.
However, Eggman's plans quickly come apart as, while Sonic and his friends crash the X-Tornado into the White House, Mr. Stewart is able to rescue the President and Christina in the confusion, allowing Sonic to send Eggman flying out of the building. Meanwhile, Topaz and Rouge head up to the Egg Moon in a space shuttle with Mr. Tanaka and Knuckles, where Knuckles is able to destroy the Egg Moon's transmitter since Rouge could not destroy the one back on Earth, ending the eclipse.
His plans foiled again, Eggman, along with Decoe and Bocoe, flee from the police, only to run into a trap set up by Sonic and his friends, resulting in the three being arrested and incarcerated, ending their threat for the time being.
"Eggman for President" provides examples of:
- Big Damn Heroes: Knuckles helps G.U.N finish off the Egg Moon's transmitter, while back on earth, Sonic and his friends corporate in having Eggman taken down by the police and sent to prison with a quiz.
- Bound and Gagged: Eggman does this to the President and his secretary after his plan is revealed.
- Breaking the Fourth Wall: The Japanese version has a ton of this during the climax, following off the previous part, with Eggman insisting he, not Sonic, is the show's real protagonist.
- Brainwashed and Crazy: The true nature of the Sunshine Balls.
- Conflicting Loyalty: Both the President and Chris are extremely unwilling to act against Sonic despite the evidence piling up against him. This is more evident in the Japanese version, where they both catch themselves for doubting Sonic.
- Did You Actually Believe...?: Even Decoe and Bocoe are genuinely convinced Eggman has turned over a new leaf, until he reveals that it's yet another Evil Plan to establish his empire; he even calls them out for thinking his hero act was actually real:Eggman: Don't tell me you metallic meatheads think that this hero act is for real. Why, I planned this crafty little coup right from the beginning!
- Dirty Coward: Jerome and his angry mob act tough when they're threatening a bunch of kids and an old man, but they immediately run for it when the S-Team shows up.
- Easily Condemned: Sonic is now on the most wanted list for destroying the Sunshine Balls. The public also turns on his friends, believing them to be just as guilty for being friends with Sonic.
- Easily Forgiven: Sonic's friends are shockingly quick to forgive the people of Station Square after they broke into their home and tried to attack them.
- Fair-Weather Friend: The people of Station Square. When Sonic looks guilty, they all immediately believe the worst of him and switch from loving him to hating him. Then after Sonic proves his innocence, they switch back to loving him.
- Go Through Me: Sam Speed and his S-Team arrive as The Cavalry and warn Jerome and the mob that they'll have to fight him if they lay so much as a hand on Chris or Sonic's friends.
- Guilt by Association: The angry mob tries to attack Sonic's friends just for being friends with Sonic.
- Hate Sink: Jerome and the rest of the angry mob. They immediately believe Sonic is evil, try to attack his friends (who have saved all their lives more than once) just for being friends with Sonic, and have no problem trying to hurt kids or an old man.
- Idiot Ball: The plot is reliant on no one, not even the most intellectual of characters such as Tails or Chuck, remembering that both the moon and the Earth are in constant orbit. If it had malfunctioned and stopped, it would not remain stationary to the planet's sunlight as a result. It takes Sonic to point this out to him, though he himself waits until he's gotten tired of fighting off the misled forces.
- Karma Houdini: Jerome and his angry mob get let off with a warning after trying to attack Sonic's friends.
- Know When to Fold 'Em: Jerome tenses for a fight, but then slumps in defeat, realizing fighting Sam and his elite lawmen is a no-win situation for him and the mob. They then break up and leave without further incident.
- Let's You and Him Fight: Sonic and Knuckles battle each other for the second time.
- Mass Hypnosis: It's revealed that Eggman's Sunshine Balls emit a subliminal message to hypnotize people into obeying him as part of his latest evil plot.
- My God, What Have I Done?: When the President finds out about Eggman's deceit, he angrily threatens to ruin him. However, Eggman gloats he can't do a thing since he decided to send all his forces onto Sonic. The dub changes the context of this exchange, despite keeping in the President's guilt ridden reaction.
- Not Helping Your Case: As Knuckles lampshades, Sonic didn't bother telling anyone about Eggman's plan before destroying it, and was perfectly willing to just spar with him and the President's forces when they came in his way. Sonic's retort is that it should have been pretty obvious.
- Only Sane Man: Sonic is the only one who realizes from the start that Eggman's Egg Moon/Sunshine Ball deal is a scam and a lie because if the Egg Moon had truly stopped rotating, then it would stand still and not keep blocking the sun; even geniuses like Tails and Chuck forgot this little detail. When Knuckles demands to know why he didn't tell them that before he went about smashing the towers, Sonic simply says, "I thought it was obvious."
- Thought They Knew Already: Sonic's reasoning for not bothering to tell anyone the real reason for destroying the sunshine orbs. In fairness, it was pretty simple physics, though it's implied Sonic was also enjoying trolling the forces trying to stop him.
- Troll: While Sonic does make the fair point that he shouldn't have had to inform everyone of the hole in Eggman's plan, he seemed to be visibly enjoying his skirmishes with the misled forces regardless, implying he fully knew the panic he would cause.
- Ungrateful Townsfolk: A large amount of people in Station Square turn on Sonic after all the times he saved them. They also turn on his friends, even though Sonic was the only one who appeared guilty.
- Unwitting Pawn: Decoe and Bocoe are genuinely disappointed when they realise Eggman's scheme was Evil All Along, having enjoyed being the heroes for a change.
- What the Hell, Hero?: No one except for Sonic knew the truth about Eggman's plans, not even G.U.N.. As a result, it isn't until Sonic explains everything to their faces that they realize Eggman fooled them again. Knuckles in turn calls out Sonic for not bothering to tell anyone in the first place, to which Sonic retaliates he thought it should have been pretty obvious to them.
- With Us or Against Us: When Sonic's friends don't tell the angry mob where Sonic is, they decide to attack them.
- Would Harm a Senior: Jerome and the angry mob try to attack Chuck along with the rest of Sonic's friends.
- Would Hurt a Child: Sonic's friends at Thorndyke Mansion mostly consist of children, and Jerome and his mob have no qualms about trying to attack them.
