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We see Stone in Robotnik's office, thinking to himself.
Stone: Hmm. The Doctor's going to be back soon, and I haven't done much to further his cause. I need to do something to show my commitment. But what?
He begins to think to himself. Eventually, his mind wanders to Angel Island and the Master Emerald. Suddenly, he snaps his fingers.
Stone: That's it! I'll steal the Master Emerald!
He begins to walk out of the room.
Stone: I'm sure the Doctor won't mind me borrowing a few of his Eggrobos to get the job done.
Later, we see Stone approaching Angel Island in an Eggmobile, flanked by a squad of Eggrobos.
Stone: Alright, all of you, spread out. Find the Master Emerald, and alert me once you do.
The Eggrobos begin to spread out across the island. One of them spots Knuckles, sleeping near the beach on Angel Island. Recognizing him as an enemy, it drops a bomb near him, before flying off. Knuckles wakes up, and throws the bomb into the air before it explodes.
Knuckles: There's only one person I know who'd try to blow me up. And if he thinks he can get away with attacking my island, he's got another thing coming!
Knuckles begins to make his way across Angel Island, battling Eggrobo's piloting Robotnik's various machines as he does. Eventually, in the Marble Ruins, he comes into contact with Agent Stone.
Knuckles: You! Where is Robotnik!? Is he to scared to fight me head on!?
Stone: Oh, I'm afraid that Dr. Robotnik isn't here. I'm just picking up a delivery for him.
Knuckles: I won't let you take the Master Emerald!
Stone: I know.
Stone begins using the machine to fire a chain through the ground, before using it to drag the machine around. Eventually, Knuckles is able to defeat Stone, causing him to retreat.
Knuckles follows him across the island, defeating more Eggrobo's as he does. Eventually, he ends up in the former Launch Base, where he comes across Stone in a smaller machine, which attempts to crash into Knuckles. After Knuckles dodges, Stone attempts to fire energy balls into the floor, which travels up the walls. Eventually, Knuckles is able to defeat Stone, causing him to retreat further into the Base. Eventually, Knuckles is able to make his way further up into the Base, defeating another Eggrobo and Stone in the Big Arms, causing Stone to activate the self destruct, causing Knuckles to land in the Mushroom hills.
Knuckles continues forward, making his way through both the hills and a rebuilt Flying Battery. Halfway through it, he runs into Stone again, this time in a spherical machine which hops around the area, firing missiles as it does. Eventually, a small spiked bomb is fired from the top of the machine, allowing Knuckles to attack it, eventually destroying it.
Knuckles moves forward, sinking the Flying Battery again, before proceeding forward across the Sandopolis. Eventually, once he reaches the pyramid, Stone emerges from the entrance in a wheeled machine, before attempting to ram into Knuckles. Eventually, Knuckles defeats Stone, causing him to fly into the pyramid, with Knuckles in pursuit.
After making his way through it, and defeating another Eggrobo, Knuckles enters the Lava Reef, before making his way to a teleporter which takes him to the Sky Sanctuary. He moves forward, finding the Master Emerald resting on a pedestal.
Knuckles: He hasn't found it yet. Good.
Stone: About that...
Knuckles turns, seeing Stone in the Eggmobile, with a claw connected to the bottom, holding Mecha Sonic.
Stone: Thanks for leading me to the Emerald! Now I have to do is take it from you after my friend is finished turning you into a red puddle!
He drops Mecha Sonic onto the ground.
Stone: Mecha Sonic, kill him!
Mecha Sonic charges at Knuckles, and the two begin to fight, with Knuckles eventually managing to defeat Mecha Sonic. However, Mecha Sonic rolls backwards, before using the Master Emerald to become Super Mecha Sonic. Mecha Sonic attempts to charge into Knuckles, before firing energy balls from his chest, causing him to lose his Super Power, letting Knuckles attack him. After a few more cycles of this, Mecha Sonic begins to float slowly through the air, before shooting out a ring of harmful rings, before he drops down, briefly losing his Super Power, letting Knuckles get a hit on him, before floating back into the air. Eventually, Knuckles is able to knock Mecha Sonic out of the sky, punching a hole through his chest, before delivering an uppercut that sends him falling towards the sea below. Knuckles turns toward Stone, who is still in the Eggmobile.
Knuckles: You wanna end up like him?
Stone shakes his head.
Knuckles: Then get off of my island.
Stone nods, before flying away from the island. Knuckles walks back to the Emerald.
Knuckles: I should probably move this thing in case he or Robotnik comes back. Now, how am I gonna get down from here?
Suddenly, he hears the sound of a plane engine coming from above. He looks up to see Sonic flying the Tornado above him.
Sonic: Need a lift, Knucklehead?
Later, we see Sonic and Knuckles meeting up on a nearby cliffside.
Knuckles: So, Robotnik managed to get his hands on a Chaos Emerald.
Sonic: Yep.
Knuckles: And let me guess: You came all this way just to ask for my help, didn't you?
Sonic: Wh- no! I just thought you should know, that-
Suddenly, the conversation is interrupted by something crashing down in between the two, knocking Sonic into a tree, causing him to fall unconscious. Knuckles looks up, seeing Metal Sonic standing in front of him.
Knuckles: Another one!? I already beat one of you guys, so this should be a piece of-
Knuckles is interrupted by Metal Sonic punching him in the face, causing the two to start fighting. Metal Sonic fires energy balls from his chest, and attempts to charge into Knuckles. Eventually, Metal Sonic grabs Knuckles by the throat, before dropping him and flying off.
Knuckles: Where are you going, you big chicken!? What's the matter, scared!?
Knuckles turns to the still unconscious Sonic, noticing a devicein his bag. He takes it, pressing a button on it, causing it to start beeping.
Knuckles: Must be some kinda homing beacon... Don't worry Sonic. I'll make sure Robotnik pays for this.
With that, Knuckles runs off, leaving Sonic behind.