Shadow and Rouge are currently flying to the Old Kingdom, which just so happens to be the G.U.N. rendezvous point. Eggman's Egg Gunners were flying all over the place, which meant bad news for the two.

Shadow and Rouge eventually get to the old castle of Soleanna, but what they saw was just a destroyed remnant of what remains.

Rouge: [With artifact in hand] The former king of Soleanna used to reside in this castle. But a major accident occured 10 years ago, and no one's lived here since.

Shadow: [Curious] Accident?

Rouge: I heard a prototype energy engine failed, which caused the accident. I think the name of the plan was...

Eggman: [Appears above them; finishes sentence] The Solaris Project. [Lowers Egg Mobile down] It was an ambitious project named after their eternal sun god.

Rouge: [Surprised] Doctor!

Eggman: It's been a while, my dear Rouge. [Nonchalantly] And of course, Shadow. Now, if you'd be so kind as to hand back the Scepter of Darkness you took from me.

The Scepter of Darkness. It must have been the artifact Rouge had, but the Egg Gunners hover down to the ground to pursue them. Only, Shadow wasn't having any of it. The Gunners start shooting and Team Dark jumps out of the way, with Rouge already on the way out. Eggman knocks her out of the air, but before she can fully drop, Shadow catches her.

Eggman: No...!

The Scepter of Darkness falls to the ground and shatters, short circuiting the Egg Gunners in the process. Shadow goes to inspect the scepter, but some kind of darkness comes out of it, causing him to gasp.

Rouge: Shadow!

The stream of darkness flies out of the scepter, flying all around the damaged Egg Gunners.

Eggman: [Frightened] It's no use! Pull back, pull back, pull back! [Flies away]

Before the Egg Gunners can follow behind the Egg Mobile, the darkness takes them out and shoots into the air, then slams right into the ground. Shadow moves out of the way and lets the darkness swim right into the floor, but what happens next was definitely a shock, especially to the Ultimate Life Form. The darkness takes shape and forms into a dark hedgehog, completely made from the shadow of well... Shadow himself.

Rouge: [Confused] What? His shadow...

???: [Evil laughter] Oh, how ironic fate can be! I would never have believed I would be resurrected from your shade! I thank you, Shadow The Hedgehog! [Bows]

Shadow: [Confused] Who are you and how do you know my name?

Mephiles: [Slowly walks towards them] I'm Mephiles. Mephiles the Dark. What, did you forget me? [Looks up at Shadow] I owe much to you, Shadow. [Brings hand up; orb appears] Oh yes. What you gave to me, I now return to you! A one-way ticket to oblivion!

The orb rises into the air and next thing the team of Shadow and Rouge notices is them disappearing. This Mephiles eventually disappears as well, now gone from the area. Meanwhile, after encountering Silver The Hedgehog, Sonic and Aeon get word from Tails that Knuckles The Echidna and Protector of the Master Emerald made his way to Soleanna to have a word with them. They make their way over to the town's warehouse, while also destroying every Egg Gunner in their path. They eventually defeat the Egg Gunners and meet up with Knuckles, who has something in his hand.

Sonic: Knuckles.

Aeon: [Salutes him] Sup, Echidna.

Knuckles: [Angered glare] I admit, I was skeptical when Tails told me you were here, Aeon.

Aeon: So I've been told. Anyway, you needed to see us.

Knuckles: [Nods] I saw Eggman on the outskirts of the city. [Tosses note to Sonic] He wanted me to give this to you.

Eggman Hologram: [Appears from note] Sonic and Aeon The Hedgehog. If you want me to return the Princess, you must give me your Chaos Emeralds. Meet me at my base in White Acropolis. [Hologram disappears]

Sonic tosses the note back to Knuckles, who fails to catch it and stumbles as he tries to grab it. It then hits the ground, and he stomps on it.

Knuckles: [Scoffs] He's pretty cocky.

Tails: It's most definitely a trap.

Aeon: Yeah, but what choice do we have? Sure, we all know Robotnik won't honor his end of the agreement, but we've got to save Elise. [Pulls out Chaos Emerald; hands it to Tails] Take this, Tails.

Tails: [Confused] Why give it to me?

Aeon: It's safe with you, and I know what you could do with the X-Tornado. Besides, I've got somewhere to be.

Sonic: [Pulls out second Chaos Emerald] You do what you need to do, Aeon, but I'm going.

Tails: [Confused] Sonic?

Sonic: Since Eggman went to the trouble of telling me where Elise is, I think I should thank him personally.

Sonic, Knuckles and Tails run into the base, but come to a circular room with no sign of Eggman or Elise.

???: You're late.

The three look up to see a glass wall, with Eggman behind it.

Knuckles: Well, we had to deal with your little pets.

Sonic: [Getting serious] Where's Elise?

Eggman: My, aren't we impatient...

Elise: [Gets brought in; worried] Sonic!

Eggman: [Sonic goes to pursue] Ah ah. You better not move. Now, the Chaos Emeralds...

Sonic pulls out exactly what Eggman wants, and they shine just as bright.

Eggman chuckled, seeing both Elise's Chaos Emerald and Aeon's Chaos Emerald.

Eggman: [Points to platform] Place them there.

Elise shakes her head in anticipation, but there was nothing Sonic could do. He placed both Emeralds in their respective spots and watches as they get brought up to Eggman, but the mad Doctor thought of everything. He pushes a button and a giant, pinkish barrier appears all around Sonic, Knuckles and Tails.

Tails: [Confused] Huh? What?

Knuckles tries taking down the barrier with his strong punches, but gets pushed back.

Eggman: It's no use. It's too powerful for you to overcome. Now allow me to introduce you to my latest creation. This is the Solaris prototype. [Elise gasps; maniacal chuckle] With this machine, I'll be able to control the flow of time itself!

Eggman pulls a lever and Sonic, Tails and Knuckles hover into the air, sending out screams. The barrier dispels and Elise drops to her knees, feeling the worst for the three.

Eggman: Rest assured... They're not dead... yet. They've just been teleported by my glorious invention to another time. Who knows where they'll end up? I could be in the distant past or far future. But my machine still requires some fine-tuning. In fact, what my machine needs in order to be complete, is your power.

Elise: [Confused] My power?

Eggman: Yes, I can finally complete my plans... [Points to Elise] Now that I have the Chaos Emeralds, and you... The Princess of Soleanna. That's all I need to revive the Flames of Disaster. And with its power, I will be able to control everything and rule the world. So, you would be wise to remain on my "good" side.

Eggman walks away and Elise puts her hands together, hoping Sonic, Tails and Knuckles are safe... that is where and whenever they are now.