[It's a stormy night where the Egg Carrier can be seen approaching Angel Island. Knuckles can be seen sitting at the Master Emerald shrine, deep in thought as his eyes are seen closed]
- Knuckles: As far back as I can remember, I've been living here, on this dark island... Always guarding the Master Emerald from anything that can harm it. I don't know why I was given this job... Why it was my fate... Destined to be here...forever! [Hears a sudden crash] What the...?
[Knuckles turns around to find a mysterious being near the Master Emerald]
- Knuckles: What's going on here? Oh no! [Notices that the Master Emerald has been destroyed] Something has happened to the Master Emerald! [Turns his attention back to the creature] Huh? Who are you? Did you do this? Ohhh, I'll get you for this!
[Knuckles tries to attack the creature but it leaps out of the way and crashes onto Knuckles]
- Knuckles: Ooomph! [Falls off of the shrine] Ugh agh! Hey, no fair! [Runs back up the shrine but the mysterious creature dissolves as a puddle and leaves] Wait! What's happening to you? Come back here! Wow! That was incredible! I've never seen anything like it! [Notices Angel Island starting to shake] Oh no! It's starting to happen. Without the Master Emerald's power, this whole island will fall into the ocean!
[Soon, Angel Island falls into the ocean, right next to the Mystic Ruins]
[Knuckles is in Station Square, presumably some time after Angel Island descended into the ocean]
- Knuckles: It's up to me to find the missing pieces of the Master Emerald. It won't be easy. Pieces flew off everywhere. Guess I'd better start looking anywhere I can.
[Knuckles has just finished finding the Emerald Shards in Casinopolis when a red orb suddenly starts to move around Knuckles; then, Knuckles is taken back in time]
- Knuckles: Where in the world am I? [Looks around] I don't remember being here before. But something about it is familiar. Hmmmm... This is very strange.
- Tikal: Father! Please don't!
- Pachacamac: Tikal, the 7 Emeralds are essential to our survival. It is for the good of all our people.
- Tikal: How can I make you understand? Attacking other countries, stealing and killing...can't be the right path to peace. No one has the right to take their holy grounds. I beg you father!
[Light engulfs around Knuckles]
[Knuckles is taken back to Station Square just outside Casinopolis]
- Knuckles: Uhh! Now where am I? [Looks around] Back in Station Square, I see. What's going on around here anyway?
[Knuckles heads into the hotel and spots Eggman heading toward the elevator]
- Knuckles: Hey, it's Dr. Eggman! [Notices Eggman holding something that is shiny] What's he got there? It's gotta be a part of the Master Emerald! Hold on! Come back here!
[Knuckles chases Eggman into the elevator and ends up in a restaurant area]
- Knuckles: Eggman! Give me back the Master Emerald!
- Eggman: Knu... Knuckles! Uhh, this isn't what you're after! [Shows Knuckles his Chaos Emerald]
- Knuckles: Huh, you're right!
- Eggman: That's okay, though. I could use you as a guinea pig to test it. Chaos! Chaos!
[The creature from earlier appears as it's name is revealed to be "Chaos" and is different in appearance from before, having become Chaos 1 since Knuckles last saw it]
- Knuckles: Chaos? It's that creature again! The same one I saw on my island. He was there when the Master Emerald was shattered, I'm sure of it. He saved me the trouble of looking for him. Now I'll get him good!
[Eggman tosses his Chaos Emerald into Chaos and Chaos grows in size becoming Chaos 2]
- Eggman: Ha ha ha ha ha! Way to go, Chaos!
- Knuckles: Hah! Changing shape won't scare me!
[Chaos 2 roars]
- Knuckles: Fine! Give it your best shot!
[Chaos reverts back to a puddle]
- Eggman: Bah! So what if you won this time. You have yet to see true powers of Chaos!
- Knuckles: Yeah yeah, that still doesn't faze me, you hear?
- Eggman: I know something that might. It's about Sonic.
- Knuckles: What? What about Sonic?
- Eggman: He's after the pieces of the Master Emerald, too!
- Knuckles: What do you mean?
- Eggman: [Starts to walk off but turns back around] You're not the only one on a wild goose chase, idiot! Why should I ruin your surprise? Ha ha ha ha ha ha... [Leaves]
- Knuckles: [After walking a few steps] I wonder what he meant by that? I'd better find Sonic.
[At Mystic Ruins]
- Knuckles: I wonder why Sonic is after the Master Emerald? I'd better work fast and get to the bottom of this.
[After clearing through Red Mountain]
- Knuckles: [Spots Sonic and Tails and notices Sonic holding something] There's Sonic! Eggman was right. What's that in his hand? It looks like a piece of the Master Emerald! He has no right to have that!
- Sonic: Hey, Knuckles!
[Knuckles tries to attack Sonic but Sonic dodges]
- Sonic: Woah! What do you think you're doing?
- Knuckles: All right! Put 'em up! Hand over the Emerald now!
- Sonic: That's not gonna happen buddy!
[Knuckles and Sonic charge at each other and the collision causes Sonic to drop his two Chaos Emeralds]
- Sonic: Ah geeze! Oh no! The Chaos Emeralds...!
- Eggman: [Appears and is laughing]
- Knuckles: Eggman! What's he doing here?
- Eggman: [Takes both Emeralds] Ha! That's all there is to it. You guys are too easy!
- Knuckles: [Notices the green Emerald is not a piece of the Master Emerald] That's a Chaos Emerald!
- Eggman: First come, first served, they say. And you served me too well for your own good! Ha ha ha ha ha ha ha!
- Sonic: You can't get away with this! [Turns to Knuckles] Knuckles, did you let him trick you again?
- Knuckles: Like, you weren't?
- Sonic: Smooth move, Knucklehead!
- Eggman: Ha ha ha ha ha ha ha... I've got 4 Emeralds now. Here, Chaos!
[Chaos in his second form appears]
- Eggman: Come here, my hungry pet! [Throws the Chaos Emeralds into Chaos turning it to Chaos 4]
- Tails: Now look what he is!
- Knuckles: No problem. I'll make him eat dirt!
[The Egg Carrier is seen appearing from the clouds and it hovers above Mystic Ruins]
- Eggman: Behold, my flying fortress! My creation, the Egg Carrier. Beware, Chaos' true power is yet to be unleashed. Ha ha ha ha ha... We shall meet again!
[Eggman is warped onto his Egg Carrier and it flies away]
- Tails: Hurry, Sonic! What are we waiting for? My workshop's close, so let's go get the Tornado and go after him!
- Sonic: Good idea!
- Knuckles: Hey Sonic! You go on ahead without me. I have some things I need to take care of.
- Sonic: No problem, Knuckles! We'll take care of everything here. Let's move!
[Knuckles runs off]
[After recovering the Emerald Shards in Lost World, the same red light from earlier surrounds Knuckles and he is taken back in time again]
[Knuckles is at the Master Emerald Shrine of the past]
- Knuckles: Where am I? This is very strange.
[Knuckles moves on forward to find Tikal talking to the Master Emerald]
- Tikal: I beg of you. Hear me now. My father is coming here soon. And I fear what may happen. You must take everyone away from here! Oh please! [After a brief moment] So, are you saying you can't leave this place? I understand... Let me talk to my father again! There must be a better way to do this.
[Tikal turns around to find some Chao]
- Tikal: Don't worry, my friends. I won't let you down. I must do something...quickly. [Runs off]
[Knuckles is taken back to the present to the Master Emerald shrine]
- Knuckles: What... I'm back in front of the altar! This is beginning to blow my mind! Wait a minute... I remember... The broken pieces of the Master Emerald... I have to restore them to where they belong.
[Knuckles heads up the shrine and places the shards of the Master Emerald onto the spot where they reunite, almost completing it]
- Knuckles: It's still incomplete! I need to find the remaining pieces. Wherever they are. [Looks into the Master Emerald and notices the Egg Carrier is shown] Hey look! It's Eggman's flying fortress. That's where the rest of the pieces must be. [Leaves the shrine] But I don't know where that ship is.
[Suddenly, a robot leaps from the mountains and leaves the area]
- Knuckles: Hey! Isn't that one of Eggman's robots? I know... I'll follow it back to Eggman's base! Here I come, Eggman!
[Knuckles follows the robot to the entrance of Eggman's base deep within Mystic Ruins]
- Knuckles: Hmmmm, just what I thought. Time to make a house call!
[The Egg Carrier takes off]
[Knuckles is on the deck]
- Knuckles: Now we'll see who's so easily tricked! I can sense the Emeralds are here somewhere!
[After walking around for a bit]
- Knuckles: Uh! What's going on?
[The Egg Carrier changes form]
- Knuckles: Ugh! This thing's always changing. [After getting into the recently drained pool] I sense the Master Emerald. It can't be far from here.
- Knuckles: The last missing piece! Alright! Now to restore the Master Emerald! [The red light takes him back into the past again]
[Knuckles is back at the Master Emerald shrine at nighttime]
- Knuckles: Oh no! Not again. [Notices an ominous red glow in the distance] What's the meaning of this?
[Knuckles heads closer and notices the shrine is on fire. Knuckles notices Tikal is on the ground and runs up to her]
- Knuckles: Hey, what happened here?
- Tikal: I couldn't...stop them. They came...and my father... I had no idea...how bad this would turn out! I'm shocked!
[Tikal gets up and the Master Emerald is shown]
- Knuckles: Look, it's the Emerald! [Tikal leaves] Wait! [Knuckles is taken back to the present]
[Knuckles is back in the pool area]
- Knuckles: Is this a dream? It's more like a nightmare! [Starts heading toward the deck] I finally found all of the missing Emerald pieces, but... I still can't figure out that creepy monster. Huh? What's that? [Suddenly is blinded by a bright light coming from the deck] Woah...
[Knuckles heads for the center area of the deck and notices Sonic and Eggman confronting each other]
- Eggman: Aarghh! Not again... I hate you!
- Knuckles: [Heading toward Sonic] Hey, Sonic!
- Sonic: There you are, Knuckles. About time!
- Eggman: I will return! [Flies away in his mobile]
- Sonic: [Chasing after Eggman] Eggman! Come back!
- Knuckles: I'd better let Sonic handle it from here. He'll do okay. Now... I must return to Angel Island and the Master Emerald. [Notices Chaos is still around and it is in it's sixth form] No! It can't be! I guess he didn't get enough the first time! You can't stop me from restoring the Master Emerald!
[After defeating Chaos 6]
- Knuckles: Yeah! You're finished! What's left now is to return the Master Emerald safely to my island.
[Soon, the Egg Carrier is destroyed and Knuckles is back on Angel Island where he uses the last remaining pieces to restore the Master Emerald]
- Knuckles: This should do it! Perfect. All is well, now! The Master Emerald and the island have been restored.
[Knuckles starts to walk off as the Master Emerald glows brightly and Angel Island is floating again]
- Knuckles: I'll probably be on this floating island forever. Guarding the Master Emerald, again. I may not know the whole story behind this. But perhaps it's better that way. I'm at peace one more.