Aeon and Sally are seen running away from the train, Elise in his arms, and back to Soleanna.
Elise: [Full of happiness] I knew it... [Aeon looks at her] I knew you'd return! You had to!
Aeon: Like I said, Princess Elise. I always stick to my word.
Sally: It'll be alright, Princess Elise. We'll get you back to Soleanna, and then we're going after Eggman.
Elise: I'm grateful, but where's Sonic?
Aeon: [Tries getting a sentence out] I don't--
Aeon jumps out of the way when he sees one of those Telekinetic blasts coming from the side, which meant Silver was here.
Aeon: [Puts Elise down] It's you again.
Silver: Where is the Iblis Trigger?
Aeon: Listen here, faker. His name's Sonic.
Silver: Then I'll deliver you to him on a silver platter.
Elise: [Steps back] Aeon...
Sally: [Blocks Elise] Stay behind me, Elise...
Silver sends an attack at Aeon, who dodges and attempts to fire his cannon at him, but gets trapped in a Telekinetic hue. Elise stands back, but gets shocked when she sees Eggman's Egg Mobile grab her again.
Eggman: So how was your little walk, Princess?
Elise gets grabbed again by Eggman and Sally tries pursuing, but fails.
Sally: Let her go, Robotnik!
Eggman: [Looks down; grins] Ah. It's good seeing you, Princess Sally Acorn. But, our time has to be cut off. [Flies off]
Aeon: [Reaches out] Elise!
Silver: [Pushes Aeon down; scoffs] Time to send you to the Iblis Trigger!
The white hedgehog goes to finish this fight, but Shadow jumps in and stops him, causing Silver to let go of his control and drops Aeon.
Silver: [Confused] Who? [Sees resemblance to Mephiles] Mephiles! Why are you getting in my way?
Shadow: [Crosses arms] I'm Shadow. Shadow The Hedgehog.
Silver glares at Shadow, once again getting frustrated that his plans have been stopped by one of Sonic's friends. Shadow turns to Aeon and nods.
Shadow: You're done here. He's mine.
Aeon: [Lost for words] Shadow...
Shadow: [Turns focus back to Silver] Go after the Princess, Aeon. You tried fighting this guy, and you failed. I'll show you the true power of Chaos Control.
Aeon was shocked and confused. Why would Shadow save him from Silver? It was all nerve wrecking, but Aeon didn't question it and decided to get to his feet and runs over to Sally, taking her hand.
Aeon: C'mon, Sally. We've gotta get to Eggman.
Sally: [Smiles] Let's go then.
Aeon picks Sally up bridal style and runs off, but she looks back at Shadow and gets worried.
Sally: You sure Shadow can stop Silver?
Aeon: To be honest, I don't know. But they don't call him the Ultimate Life Form for nothing, so I've got to trust him, Sally. [Smiles] But we've got nothing to worry about.
Shadow and Silver stand face-to-face with one another, each taking breaths of exhaustion, but Silver wasn't about to let it end here. He lets out a frustrated scream and goes to attack Shadow, but the Ultimate Life Form was ready.
Shadow: [Pulls out Chaos Emerald] Chaos Control!
Time freezes and Shadow goes behind Silver and kicks him in the back of the head, sending him down. The white hedgehog gets up and looks at the black and red hedgehog with anger in his eyes, now completely enraged.
Silver: You...
Shadow: Don't bother. With a Chaos Emerald's power, I control time and space. You can't break free.
Silver: [Shakes head] I won't give up! It all depends on me! Can't lose... Not when I'm so close!
Silver pulls out his own Chaos Emerald and lets out another scream, but the two were thinking of the same thing this time.
Shadow & Silver: Chaos Control!
The two move out of the way as a vortex appears, shocking the two.
Silver: Huh?
Shadow: You... induced a Chaos Control.
Silver: I won't let anyone get in my way! [Clutches fists] I'll change the past and save the world!
Shadow: [Shakes head] Mephiles isn't trying to help you to create a better future... He's trying to eliminate the past.
Silver: [Confused] What? What are you talking about?
Shadow: [Steps closer] To discover what happened, it seems we must see what took place 10 years ago. Follow me if you want the truth.
Shadow jumps into the vortex and leaves Silver to think about his decision. He eventually nods at this and jumps into the vortex after Shadow, wanting to know the truth behind Mephiles' motives. They appear in a corridor that goes two ways. Behind them, there's a huge power surge and it was here where the two hedgehogs would learn what really happened.
Soleanna Scientist 1: An electromagnetic pulse has just been generated! Injecting decompression agent! No, the level's not dropping! A spatial meltdown is inevitable!
Soleanna Scientist 2: My Lord, it's too late! We've got to take shelter!
The main scientist behind the Solaris Project, Elise's father, was at the controls of the machine and is completely confused with the power surge.
Elise's Father: [Slams fists on controls; confused] Why, Solaris? Why do you refuse to listen to my voice?
???: Father!
He turns to the sound of a little girl calling out to him.
It was a young Elise. This was the incident she mentioned to Sonic before, and Shadow and Silver were viewing it first hand.
Elise's Father: Elise!
The core reactor of the Solaris Project goes off and sends out an explosion, one of which Elise's father gets in front of his daughter and blocks the blast. Shadow and Silver hear the explosion from the corridor and run ahead, only to find the lab destroyed. They jump down into the lab and a yellow spark above a black shadowy goop.
Silver: [Shocked] Is that!? [Flame appears] That flame... It's Iblis!
Shadow: And the black shadow is the original Mephiles.
Silver: [Even more shocked] That's Mephiles!? [They try getting away] They're escaping!
Shadow: We'll have to split up. I'll pursue Mephiles.
Silver: [Nods] OK. Then leave Iblis to me!
Elise's Father: [Stops them from leaving] Wait. [Struggles; holds Scepter of Darkness] Seal it with this...
Silver: Hurry! [Runs off]
Shadow takes the Scepter of Darkness and chases after Mephiles, ready to pursue him and seal him away in the artifact.
Mephiles attempts to get away, until Shadow brings out his Chaos Emerald and prepares...
Shadow: Chaos Control!
Mephiles: [Stops and groans] ...What? ...Stop! [Scepter of Darkness hovers in air] Who... Who are... You?
Shadow: [Sealing Mephiles] I'm Shadow. Shadow The Hedgehog.
Mephiles: [Being sealed in Scepter] Shadow... Your face... Your form... I will remember. Your death... Certain... You... will die!
The Scepter of Darkness drops to the floor after sealing Mephiles and Shadow picks it up, now with the means of sealing Mephiles for good. Meanwhile, Silver pursues Iblis, stopping it from getting away before it can cause trouble.
Silver uses his Telekinesis to keep Iblis in his place, stopping the flame from going any further. As he starts to struggle, the King comes into the room, holding Elise in his arms.
Silver: Hey! What are you doing? You've got to leave!
Elise's Father: I have my duty. This Living Flame has been entrusted to the royal family. [Walks over to Iblis] The Flames of Disaster will awaken if nothing is done! That must not happen. [Sets Elise down; brings out Chaos Emerald] Eternal Sun! The Living Flame that has been entrusted to the royal family! Fall into slumber with a royal soul!
Iblis gets sucked into the Chaos Emerald and then goes straight into Elise, sealing itself inside of her. This is why she's been told not to cry, because she'd be releasing the Flames of Disaster if she did.
Elise's Father: [Brings Elise to Silver; drops to knee] I'm sorry, but... Can you take her to a safe place? [Strokes Elise's hair] That's a good girl, Elise. Remember, be brave. Don't cry, no matter what happens. Otherwise your tears will call forth the flames inside you... Become a strong queen who doesn't cry no matter what happens. And... Live... happily...
The King falls down to the ground, now dead at Silver's feet. The white hedgehog looks at Elise and then up at the sky, knowing exactly what he's got to do in order to seal Iblis. After awhile, he takes Elise outside of the Old Kingdom and looks out at the sunset. Shadow eventually comes out, holding the Scepter of Darkness.
Silver: Did you do it?
Shadow: Yes. And you?
Silver: [Nods] ...Yes. The "Flames" are properly sealed. It's done.
Silver sets Elise down on the ground next to a nearby tree, and Shadow places the Scepter of Darkness down next to her.
Silver: [Confused] You're going to leave it behind?
Shadow: Yes, I already know what becomes of it in the future... [Brings out Emerald; stands up] It's time to return.
Silver: [Pulls out second Emerald; stands up] Yes... Of course...
The two nod at each other and know what they've got to do.
Shadow & Silver: Chaos Control!
Shadow jumps through the vortex and leaves Silver, who looks back to Elise, who sleeps peacefully next to the tree. He goes to jump through it, but hears the girl mutter something.
Young Elise: [Silently] Father...
He puts the Chaos Emerald down and wraps her hands around it, smiling at her.
Silver: [Remembers Blaze's wording again] It's a lucky charm.
The white hedgehog finally jumps into the vortex, leaving Elise to sleep with the Chaos Emerald in hand and the Scepter of Darkness right next to her.