At Soleanna, a Soleanna Royal Guard is conversing with two citizens. A shadow of the Egg Carrier is seen and the three turn to look at the Egg Carrier flying above the city. Citizens begin to panic as Eggman makes his announcement.

"Princess Elise, ruler of Soleanna... By refusing to negotiate with me, you have forced me to take drastic actions."

Amy is seen in the crowd witnessing the Egg Carrier before turning to run away.

"Meet me at the specified point alone 4 o'clock today. Failure to do so on time, will result in my leveling of this city so that nothing but ashes remain!"

Elise stands outside on the balcony of her castle as she listened to this.

"Miss Elise...!" Elise's lady-in-waiting exclaimed.

"I cannot allow harm to come to my people."

As the Egg Carrier flies closer in the background, Elise turns to leave. She stops.

"Miss Elise...!" Elise's lady-in-waiting 2 exclaimed.

"It is my duty as Princess of Soleanna to go... There is no other choice."

"No. There's always a choice."

Elise looks up and was surprised to see Y/N on top of the roof of the castle. Y/N was somehow teleported to Soleanna where the castle was and on time to hear Eggman's threat announcement.

"Y/N! You've returned!"

Y/N jumps off the roof and grabs her hand.

"Come! It's not safe here now."

"OK!"

Y/N carries Elise in bridal style and jumps up to the roof, seeing the Egg Carrier following them. She slide down the roof, holding Elise close. She swung herself from the pillar and lands on the ground with a loud thud. Y/N looks around to see the robots surrounded them. Eggman must have notice Y/N was here and summon them to stop her. She took out her sword and swiftly slices them with one swing as their parts fall off and exploded. Y/N rocket roller skates away as fast as she could.

"Y/N! Watch out!" Elise cried out.

Y/N turned to see the claws coming down to grab them. She quickly dodged them, not letting him take Elise away or else something bad will happen. Just as she thought they are close to escaping, a shadow portal was brought out from the ground. Y/N didn't notice it until she fell into the portal, releasing Elise. She fell to the ground and gasped to see Y/N falling into the shadow portal. Elise gets up and tries to come after her, but the portal already disappeared before she could reach her.

"Y/N!!"

In fear, Elise turned and the claws grabbed her and pulled her into the Egg Carrier.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

New City, day. A Time-Space rift appears, depositing Shadow right in front of Rouge.

"You're back sooner than I expected. Omega is still in pursuit of Mephiles. So, where's the kid? What did you find 10 years ago?"

Rouge looks around to see Y/N is not with him.

"Say, where's Y/N?"

"I need you to access GUN's database. Specifically, find out what materials the Scepter of Darkness was made from." Shadow said.

"Sure. But you haven't answered my question yet!"

Shadow turned to her.

"I found the means to seal Mephiles."

Shadow walks away with Rouge right behind him.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Back at present-day Soleanna, the portal opens up, and Silver drops to the ground in front of Blaze, who looks at him.

"Blaze..."

Blaze crosses her arms.

"What did you see?"

Silver looks down and pauses for a second.

"Y/N's right. The Iblis Trigger... wasn't Sonic the Hedgehog."

"I see..."

Crowds of people noise. Silver turns around at the commotion.

"They're quite noisy."

"Yes. I heard that the Princess here left for Dr. Eggman's base in response to his earlier threat." Blaze said.

Silver is surprised.

"What if his ultimate objective was to release Iblis?"

Blaze turns to him in surprise. She then adds something she almost forgot to mention.

"Not only that, but Y/N the Hedgehog came to rescue her. People have been talking about that. They said that she was helping her get out of the castle while dealing with the robots, but then she suddenly disappeared."

"Disappeared?" Silver asked, turning to her.

Blaze nods.

"They said they saw her when she was close to bringing Elise out to safety when something pull her down and never come out. Elise was then taken away after by Eggman."

"That's odd... Could it be...?"

Silver gasped, remembering Y/N's words.

"He even tried to kidnap me for no reason."

"Mephiles...!"

"What?!" Blaze gasped.

They both nod at each other and run off. Silver hopes he was wrong, feeling worried for Y/N.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Y/N woke up to find herself in the dark room. She sat up and looked around. She was about to stand when something holds her down with a loud shackle. Y/N looks down to see her wrists chained up attached to the ground. She tried to pull them, but it was hard and it's hurting her.

A dark chuckle was heard, causing her to turn to see Mephiles walking in. She could tell that he's smirking, even though he doesn't have a mouth. Once he's close, he lean down to her level and grip her chin.

"How are you, my dear?"

Y/N turns her head away with a glare.

"Not good. Let me go!"

Mephiles laughed.

"Hmm... maybe I will. Not. Hahahaha!!"

"Why did you bring me here? What do you want from me?"

"Oh, Y/N. Didn't I tell you? To rule over the world and time with you by my side. Once my plan is settled, I can teach this world a lesson. Make them pay for what they deserve. Give them a war they want."

"The plan? What plan?"

Mephiles gave her a crazed look, making her flinch.

"Your friends are falling into my trap. Why did you think I brought Silver and Blaze in time? Why was Eggman searching for the Solaris Project? And the seven Chaos Emeralds?"

Y/N put two and two together before she gasped.

"No way... You..."

"Ohohoho, yes, Y/N. You're quite smart. I like it. After I collect all Chaos Emeralds, I will strike and kill Sonic! And Elise will release Iblis so I can become one powerful of them all!"

Y/N's body went pale as her eyes widen in fear and anxiety. Mephiles noticed this and grabbed her face for her to face him again.

"You will be by my side whether you like it or not. There's nothing you can do. I have everything all planned out before you and your friends. No one can stop us."

Y/N glared at him.

"You won't get away with this. My brother and my friends will find a way in time and they will stop you!"

Mephiles looked shocked before he chuckled darkly.

"You are... so amazing..."

He slowly brought out his finger claw and lightly traces it down to her cheek, causing her to shiver. He then stroke her front hair and quills. Y/N tried to move away, but the chains held her there as she was forced to be touched by him. He finally stoppped and got up, walking away.

"I have business to deal with. See you soon, Y/N. And don't bother trying to escape. There's no way out. Too bad you won't have... this."

Mephiles pulled out Y/N's crystal necklace.

"My necklace!" Y/N gasped and noticed her weapons are gone too, causing him to laugh.

"Have fun."

Mephiles then disappeared. Y/N sighed and lied down, curling herself up as she listens to nothing but being surrounded by darkness.

"Sonic... Shadow... Silver... Where are you guys?...."

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On the day in Wave Ocean, Omega is shooting Mephiles with limited success.

"Heh. This only proves you were created to stop Shadow, the ultimate life form."

Omega looks at him confusion.

"Don't tell me you didn't know. You may have been programmed by humanity, but what you did to Shadow in the future, that was your..."

In anger, Omega transforms his hands into gating guns and shoots Mephiles who after taking all shots disappears in a puff of smoke laughing. Shadow and Rouge arrive on the scene.

"What just happened?" Rouge asked.

"Shadow."

Omega turns to Shadow.

"The one that defeats and seals you in the future... is me."

Shadow looks at him with wide eyes as Omega explains his story.

"It's... It's so unfair! Shadow's always here to defend the world! Despite that!"

"Eventually, when something or someone is seen as too powerful... It is seen as a threat, and then the world becomes its enemy."

Shadow walks away.

"Shadow... Even if you believe everyone in the world will be against you. Know that I'll always remain by your side. Remember that." Rouge said. "Don't forget that Y/N will always be there for you as well."

Shadow stops walking for a sec and nods.

"I will."

He then resumes walking when Omega stops him.

"Wait. I have something I need to tell you, Shadow and Rouge. And I believe you're not going to like this."

Shadow turns to him.

"What is it?"

Omega pauses and then eventually says something that shocks Shadow and Rouge.

"It's Y/N. She's been... kidnapped."

"What?!"

"That can't be! She's too tough to be captured!"

"I'm afraid that's not all true. Mephiles took her. I manage to scan him and his memories and saw her in chains. In the darkness. Being tortured and... touched... a lot."

"Mephiles...!" Shadow growled, clenching his fist. "What does he want with her?"

"Not sure. It can either be her crystal or just her." Omega said.

"We have to go save her!" Rouge exclaimed with a glare.

"I agree."

"Then let's not waste time."

Shadow, Rouge, and Omega begins running off. Shadow will find her and seal Mephiles once and for all.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Eggman traps Elise inside the Egg Carrier and she is sitting on a chair.

"You've wasted so much of my time. If you had cooperated with me earlier, I wouldn't have to do this. Y/N is a fool to come and rescue you and look where that got her. She's no longer here."

"What are you trying to do, Dr. Eggman? Why do you wish to revive the Flames of Disaster?" Elise asked. "As for Y/N, she'll come for me. She'll find the way."

"I doubt it. And to answer your question... Did your parents ever disclose to you anything about Solaris? Solaris's secrets are in his eternal flames. His power... can change time, and even manipulate the fabric of time itself. I wish to obtain this power and dominate everything in this world. From the past all the way to the future!"

"You wish... to rule over... Time?"

"Yes. Truly. And the secret... It remains dormant in you, Princess."

Eggman proceeds to his ship's interface and begins inputting commands.

"The Princess of Soleanna and the seven Chaos Emeralds... Once I have everything, the fate of the world will change. And one of the beautiful gems is just ahead."

"Chaos Emerald located." Mother Computer said.

"Finally... Now, let's go collect that Chaos Emerald."

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Sonic runs through the Tropical Jungle when Eggman's mechs arrive to attack him. He slides and sees them, prepared to fight them, and one of them raises a gun to him when all the robots are grabbed by a Psychoshock, and Silver drops down and uses blasts from both hands to knock them all out, causing them to explode on the ground. He then turns to Sonic.

"You look like you're in a hurry."

Sonic crosses his arms.

"...So what's going on?"

Silver pauses.

"Circumstances have changed."

He turns to Sonic again.

"I need to rescue the Princess and Y/N."

"Sis? What happened to her? Where is she?"

"I might be wrong, but she's been captured. And it's not Eggman. And we need to find her after we save the Princess."

Sonic nods in approval, then he gives him thumb up and runs off, and Silver follows.

"Silver, we don't have time. Let's get to Elise right away. Then we'll find my sis."

Silver nods as they ran throughout the way as fast as they could as they can't let Elise have a same fate from the future.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Inside the Egg Carrier, an alarm is going off. Eggman is frantically typing on the keys at his interface while Elise watches with worry.

"Huh? The engines are malfunctioning."

Elise stands up.

"What's this? Stop all engines now!"

There's no response. Eggman pounds on his interface in frustration and horror.

"...Why is this happening? No! We're about to crash!"

Elise's mind immediately went to Y/N and Sonic.

"Y/N... Sonic..."

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

As Sonic and Silver make it through Kingdom Valley, the Egg Carrier, engulfed in flames, falls through the dark clouds near a hilltop and plunges downward. As Sonic, Silver and Blaze arrive, an explosion is heard, and they stop at the sight of the Egg Carrier crashing onto a hilltop.

"Elise!!"

Sonic drops to the ground in despair and slams his fist in anger and grief. Silver and Blaze are in mourning for Elise. But then Silver looks up and realizes something, then looks at Sonic.

"Wait, there's still a way to change this."

Blaze looks at him, and Sonic is recovering from grief and loss and looks at him.

"If we return to an earlier point in time, we'll be able to save her. And somehow find out where Y/N had disappeared."

Sonic recovers and takes a look at the hillside where the Egg Carrier crashes, then gets up.

"I understand."

Silver holds out the white Chaos Emerald, and Sonic holds out the turquoise one. He walks up to Silver while Blaze is watching. Both hedgehogs nod at each other and hold the emeralds aloft.

"Chaos Control!!"

The light emerges from the emeralds and splits up, opening a space-time rift. Both hedgehogs look at the portal, and Sonic quickly runs and tosses the turquoise emerald to him.

"Silver!"

Silver catches the emerald with his left hand.

"I can handle this myself. Besides, you've got somewhere to go, right?"

Silver is amazed.

"You..."

"I'll make sure to change Elise's fate. And find my sis."

Sonic raises a fist and looks at Silver before continuing.

"And that in turn should change your future, too."

Silver, with a Chaos Emerald in each hand, nods in agreement as Blaze puts her hands on her hips in wonder. Sonic gives a thumb up.

"Thank you, Silver!"

"Yeah... Just save her. Find Y/N."

Sonic nods and jumps into the rift. Silver and Blaze turn and nod at each other, then both jump into the portal one by one.