[The cutscene begins with Angel Island falling to the ocean again and ends here.]
[The cutscene begins with Eggman making his way through the jungle of Mystic Ruins in his Egg Mobile.]
- Eggman : Ooooh... I hate that Sonic! He always seems to get in my way! But I bet he can't foil my master plan. [Notices Chaos on the ground] Chaos!
[Chaos then attacked Eggman.]
[The cutscene begins with Knuckles questioning himself.]
- Knuckles : The Master Emerald is where it belongs. But Angel Island is still falling! This doesn't make any sense. Maybe... Those Chaos Emeralds... that I brought back with me... have something to do with what's happening. I'll take them to Sonic for his advice. [Noticed Eggman lying on the ground] Eggman!
- Eggman : This is terrible! Ch- Chaos is........
- Knuckles : Is what?
[Chaos appears and attacks Knuckles.]
[The cutscene turns to Sonic who was relaxing by a tree.]
- Sonic : Yawn. Guess Eggman's learned his lesson... yep! And maybe I'll take another vacation somewhere.
- Tails: Son-ic!
- Sonic : Hey there, Tails! Did you find the Tornado 2?
- Tails: Never mind that. Get up and follow me. Angel Island is falling again!
- Sonic : Hey, no way! Who blew it this time?
- Tails: I don't know, but we'd better hurry!
[Sonic and Tails then arrive at Angel Island, where they see Knuckles and Eggman lying defeated on the ground near the Master Emerald's shrine.]
- Knuckles : Sonic... uhhh, sorry!
- Sonic : Knuckles! And Eggman? What happened here?
- Knuckles : He stole my Chaos Emeralds! And Chaos is still alive!
- Sonic : What?!
[Eggman gets back to his feet]
- Eggman : Aaarrgh! He's not gonna get away with this!
- Knuckles : Hey Eggman! Wait up!
[Eggman gets back in the Egg Mobile and roars away]
- Knuckles : Sonic... Chaos is a fearsome beast! If he gets that last Chaos Emerald, we're done for!
- Sonic : No need to explain, we'll get on it! Tails?
- Tails : Right!
- Sonic : Wha...?! Aw, Gee...!
[Sonic is sent to the past by Tikal.]
- Sonic : This place... It looks familiar! It's not a dream, after all.
[The cutscene shifts to Tikal.]
- Pachacamac : Get out of my way!
- Tikal : No Way!
- Pachacamac : Did you hear what I said?
- Tikal : I won't obey!
- Pachacamac : We need those 7 Emeralds to give us total power! It's power for the people And... They are your people too, you know! We must get that Emerald!
- Tikal: Greed is our enemy! Once it starts, you will always want more! Please don't do this. I beg you!
- Pachacamac: Bah! I don't listen to the words of a child. Ready, men! Charge!
- Tikal : Father!
[The Altar of the Emeralds comes under attack from the Knuckles Clan, who knocks Tikal to the ground and injures many Chao. Sensing what happened, Chaos becomes infuriated. The Chaos Emeralds circle the Master Emerald, then Chaos rises to confront Pachacamac and his soldiers as they reach the Master Emerald, causing them to recoil in fear.]
- Pachacamac: Aaaaagh! It's a monster!
[With a thunderous roar, Chaos unleashes its wrath on the Knuckles Clan and everything whites out.]
- Pachacamac: Noooooooo!
[Sonic heads over to Tikal.]
- Sonic: Hey, are you all right?
- Tikal: Uh... I think so. Oh my gosh! No!... No!.... No!....
- Sonic: Wait up!
[Tikal goes to the shrine and Sonic follows her.]
- Tikal: The 7 Emeralds are the servers. Chaos is power, enriched by the heart. The controller serves to unify the chaos. Uhh... The 7 Emeralds can change our thoughts into power. If this Emerald controls that power... Please, you must stop him!
[Sonic returns to the present day.]
- Tails: Sonic! Wake up!
- Sonic: Ahhh... I was on a snooze cruise, I guess!
- Tails: Good thing you're okay. You just sort of conked out, there. Knuckles left already. Come! We gotta go after the last Emerald!
- Sonic: ?... Lead the way!
- Tails: It should still be on board the Tornado 2!
[Sonic and Tails head over to Big's hut and spot the Tornado 2.]
- Tails: Look It's the Tornado 2!
- Sonic: Yeah, so let's get the Chaos Emerald and leave!
[Chaos appears and takes the Emerald from the Tornado.]
- Sonic: What? No! He's got the last Emerald!
- Tails: Now what do we do?
[Station Square is hustling and bustling with traffic and pretty much another normal day. In the sewers under the city, the water begins to ripple and soon begins to form into waves that have the troughs between them become deeper and deeper. Above, no one is aware of what's happening. Back in the sewers, water begins to flood the tunnels, while above ground, manhole covers begin to be blown clean into the air as water erupts from them, causing panic as cars screech to a halt to avoid hitting the geysers, the streets begin to crack and fissure, and water begins to blast out of buildings, shattering windows and flooding the streets before a huge tsunami roars over the buildings. When it is all over, the city is now a flooded wasteland. Several windows on one wrecked building continue to blow out before a huge rush of water bursts out before reforming into the head of Perfect Chaos. The beast lets out a loud roar before zooming in on its eye as it opens to look around with its reptilian pupil.]
- Sonic : If I wasn't just dreaming, that monster is a real menace!
[Sonic, now realizing how vicious Chaos really is, spots the Egg Carrier 2 from the corner of his left eye. Eggman then attempts to engage Perfect Chaos in combat.]
- Sonic : Eggman! Looks like he's after Chaos, too!
- Eggman : This Egg Carrier 2 was made because something like this could happen. You have defied your master, stupid beast. Now you must be destroyed at all costs!
[Eggman opens fire on Perfect Chaos, but Perfect Chaos demolishes the Egg Carrier 2 with a massive beam of energy. Eggman is flung away in his Egg Mobile after the Egg Carrier 2 crashes and explodes in a ball of fire.]
- Eggman : Aaaaahhhhh!
- Sonic: I've had enough! Who do you think you are, anyway?
- Sonic: Oh, it's you! The one... who sealed Chaos... in the Master Emerald! Tikal!
- Tikal: [Takes physical form] My heart has always been in the Master Emerald, along with Chaos'. Now he's filled with anger and sadness. And If it goes on, he'll eventually destroy the world, like he did before!
[Perfect Chaos lets forth a terrifying roar and discards the now powerless Chaos Emeralds.]
- Tikal: Look! he's absorbed the Emerald's power! He must be sealed in the Master Emerald, NOW!
- Sonic: How can that help? It won't change how he feels inside, will it? His heart will still remain in turmoil and his anger just won't vanish! He'll just be trapped forever!
- Tikal: What choice do we have?
- Amy: Hey, Sonic!
- Sonic: Amy!
- Amy: Here, take this! [Hands out a Chaos Emerald]
- Sonic: Hey guys, what's up?
- Tails : Chaos only used the negative power of the Emeralds. Sonic, you should be able to harness their real power!
- Knuckles: As much as I hate to admit it, I think Tails is right about this!
- Tails : Negative forces aren't the only way to empower the Chaos Emeralds. Our positive feelings toward each other can make them work. Our hearts together form awesome power.
[Sonic closes his eyes and uses the positive feelings of his friends and the citizens of Station Square to restores the Chaos Emeralds power and transforms into Super Sonic. He then flies off to engage Perfect Chaos in battle.]
[Chaos is reverted to his normal form, Chaos 0. He spots several of his organic kind, the Chao, and knows of their peacefulness.]
- Knuckles : Chaos has changed again. This time for the better.
- Tails : Yeah! Super Sonic must have neutralized it, so it's nice again
[Tikal arrives before Chaos.]
- Tikal : These are the chao you were protecting. They stayed alive for generations and now live peacefully with humans. The fighting's over. Harmony's restored, and life goes on. [Turns to Sonic and company] Thank you so much!
[Tikal and Chaos levitate into the air and disappear in a flash of light. Sonic notices Eggman flying away.]
- Tails : All's well that ends well, right? Sonic?
[The scene shifts to Sonic who jumps between the flooded buildings. Credits roll.]