Sonic, Y/N, and Tails arrived at a seaport in New City and encounter Knuckles. Knuckles is seen holding a card.

"Knuckles." Sonic said.

"Hi, Knuckles." Y/N greeted with a smile.

"Hi, Y/N. I saw Eggman on the outskirts of the city."

Knuckles hands her the card.

"He wanted to give this to you and Sonic."

Sonic and Y/N looks at the card and a holographic message from Eggman shows up.

"Sonic and Y/N the Hedgehog. If you want me to return the Princess, you must give me your Chaos Emerald. Meet me at my base in White Acropolis."

The recording ends and Y/N hand the card back to Knuckles, who caught it before dropping it and stomping on it with his shoe.

"Huh. He's pretty cocky." Knuckles scoffed and crushed the card.

"It's most definitely a trap. I don't think Eggman will honor his agreement." Tails said.

Y/N looks at the Chaos Emerald and looked at her brother.

"We're going."

Sonic nods in agreement.

"Y/N?" Tails said.

"Since Eggman went to the trouble of telling us where Elise is. I think we should thank him personally." Sonic said.

Y/N turned to see three robots coming down from their flight.

"We've got company, boys."

She brings out her katana and charges one of them and slices them off while Sonic spin dashes at the two robots that are flying.

"Eggman's mechs!" Tails exclaimed.

Knuckles help fight off the robots as he punches them, knocking the robot into each other. As they were fighting, they see big red lasers blocking a big entrance of a cave.

"We'll have to beat all the enemies to get through here."

Y/N nodded and flipped over the robots and slashes them into pieces and threw her katana at another that was coming behind her as it destroyed its core, leaving a hole out in the open. The robots collapsed as Y/N jumped off the falling robot and landed next to her brother and her friends as they had destroyed all of them.

"Good riddance." Knuckles sighed in relief.

"Piece of cake! No sweat." Sonic grinned.

"Let's go. We have Elise to save." Y/N said, already rocket skating ahead of them.

"Hey!" Knuckles exclaimed, running after her.

"Y/N! Wait for us!" Tails said, flying after her along with Sonic who runs along, shaking his head at his sister's impatience.

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

Silver sits down at the harbor steps in New City, still in wonder over Sonic for a long time. Just then Blaze arrives, and puts her hands on her hips.

"So this is where you are. I've been looking for you."

Silver hears her voice, but turns his head back to the shore, still pondering. She walks up to him on the steps and looks at him closely as he ponders.

"What's wrong?"

Silver sighs.

"Well, uh, Blaze. To kill someone to save the world..."

He turns his head to the shore again.

"Is that really the right thing to do?"

Blaze puts her hands on her hips again in disappointment.

"You're so naive. Whether it's right or wrong, I can't really say... But what I do know is..."

She crosses her arms.

"If we don't take this chance, the future will remain exactly as it is."

Blaze makes a sad face, and Silver looks up to her and nods, then gets up.

"Since he and Y/N are after Dr. Eggman, let's sneak into Eggman's base. Maybe we'll learn something new."

"Who's Y/N?"

"Sonic's sister."

Blaze looks surprised.

"He never mention about him having a sister. Is she a part of this?"

"No. She's not. But for some reason, she keeps telling me that he's not the enemy. She even defended Sonic with love, passion, and honor. I feel like she's telling me the truth..." Silver said.

"Whoever she is and what she's telling you, I hope you're right."

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

Sonic and Y/N are snowboarding together in the snowy forest, heading towards Eggman's base. They dodge the shooting from the robots that are aiming towards them. Y/N did a flip over the big rock and landed perfectly while Sonic spins his snowboard and landed next to her. They sled down every course from a giant snowball and robots that keep coming their way. Once they landed, they finally got out of their snowboard and charged the robots and destroyed them. Sonic and Y/N zooms in.

"This is a pretty cold place for a base."

Y/N and Sonic destroys more robots while taking out barrels and once they destroy them, they see lasers blocking their way. They easily broke down the ice that was under them and made it through.

"There should be a switch somewhere." Tails said.

Sonic and Y/N jump over and under the rolling spikes as they head towards the giant doors that opened for them. Tails told them he'll take care of something as he flew up and destroyed some searching lights that keeps an eye on any spy while destroying the robots as Sonic and Y/N follow him. Once they made it up, Sonic told him that he and his sister will take it from here. They zoom off again as they jump onto the robots and boosted themselves up over the giant laser gate. They went up the snowy hill and jumped high over the robots and searching lights and landed on the pipe as they slide through. They eventually made it to their stop.

Sonic, Y/N, Tails, and Knuckles arrive at Eggman's base.

"You're late." Eggman said, looking down at them from an upper viewing area.

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

"Where's Elise?" Y/N demanded.

"My, aren't we impatient..."

Eggman grabs Elise and is holding her by his side.

"Y/N! Sonic!"

Sonic, Y/N, and their friends get ready to fight.

"Ah ah. You better not move. Now, the Chaos Emerald..."

Y/N takes her Chaos Emerald out.

"Place it here."

Eggman points to a capsule that rises from the ground while Elise shakes her head. Y/N places the Emerald in the capsule and it recedes back into the ground. Eggman smiles wickedly before he then presses a button on a control panel next to him.

"Hmph!"

A pink force field generates from the ceiling, surrounding Sonic, Y/N, Tails and Knuckles.

"Huh!? Wha-!?" Tails gaped in shock.

"Wha?!"

Knuckles tries punching the field but gets knocked back.

"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 while Eggman laughs and pulls a handle on a nearby control podium.

"With this machine, I'll be able to control the flow of time itself!"

Sonic, Y/N, Tails and Knuckles are sucked upwards by the machine.

"Whooah!"

"Waaahhh!"

"Ahhhhh!"

"Arrrrrhhhh!"

The force field disappears along with Sonic, Y/N, Tails, and Knuckles. Elise leans against the window in despair at what she just witnessed.

"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? It could be 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."

"My power?" Elise questioned.

"Yes, I can finally complete my plans... 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 off. Elise puts her hands together to pray as she looks skyward.

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

Back in Crisis City, Shadow and Rouge are in a computer room.

"I'm in... I've pinpointed our location, It's..."

Rouge taps on keyboard and screen appears.

"No... that's not possible... We're still in the Doctor's base. But how can that be? Wait, there's no doubt now!"

"So, it's not where we are..." Shadow said.

Rouge taps on keyboard and more information appears on the screen. Rouge gasps.

"It appears we've gone through time... doesn't it?" he guessed.

"Yes... Approximately 200 years. Maybe more, depending on when this database was last updated. Well, at least we know we've arrived in the future. That means this Mephiles character has the power to control time."

"His power feels very similar to my own Chaos Control. But..."

Shadow and Rouge hear bumps in the next room.

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

At a ruined future of the same location, Sonic, Y/N, Tails, and Knuckles fall down from the machine in the top of the room. Sonic and Y/N lands on their feet. Y/N looked up to see Tails and Knuckles falling and quickly caught both of them with each hand without any problem.

"Phew... Thanks, Y/N."

"You're surprisingly strong."

"No problem."

Y/N placed Tails and Knuckles down as they started to look around.

"Where are we?" Tails asked.

Someone approaches the group from a higher ledge.

"Oh, look who's here! I didn't expect to see you guys."

Sonic, Y/N, Tails, and Knuckles look up and see Shadow and Rouge.

"Rouge! Shadow!" Y/N exclaimed in surprise.

"Hi, cutie. Long time no see!" Rouge waved happily.

Shadow nodded to Y/N, happy to see her too.

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

Sonic, Y/N, Shadow, Tails, Knuckles, and Rouge look over the ruins of Crisis City.

"This is the distant future, far removed from our own timeline." Shadow explained.

"Woah..." Y/N gasped. "This place looks terribly destroyed... and abandoned."

"The future? Then that means Eggman's machine can control time!" Tails exclaimed.

"Eggman's got some nerve dropping us here." Sonic said with Y/N nodding in agreement.

Knuckles kicks a rock.

"Now, how can we get back to our own time?"

"You need a space-time rift, but this requires a lot of energy." Shadow said.

"I see. You mean using your Chaos Control will..." Sonic started, getting where this is going.

"Yes, but that alone is insufficient."

"Okay Shadow. It looks like we need to work together." Y/N said.

Shadow nods. Rouge does as well, knowing that this will require teamwork between Team Heroes and Team Dark to return to the present. Y/N decided to go with Shadow and Rouge much to Sonic's displeasure while Tails and Knuckles whine that she won't go with them. She assured them that she'll be fine. Shadow and Rouge smiles and points out since there's only two of them, they could use one more partner. Sonic eventually let her be while looking at Shadow as a warning for no touchy with his sister. Shadow simply rolled his eyes as they all parted ways.

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

Y/N couldn't believe this and was actually glad she went with Shadow because she's flying in a hang glider! Shadow was flying beside her as he fired the incoming fire phoenixes. They dodged the floating abandoned buildings as they shoot off the fire phoenixes along the way until they stopped and landed. Shadow and Y/N jumped and took down more fire phoenixes as they jump up high to the broken road and up to another abandoned building. Y/N almost flinched to see what appear to be a giant fire worm as Shadow easily took it down before she could. Shadow gave her a wink, making her roll her eyes. After fighting off more fire creatures, they stopped to see a automobile.

"It looks like that Armed Buggy still runs..." Shadow said, looking at it.

"Huh?"

Shadow hopped into the Armed Buggy and started the engine. Y/N was shocked.

"Come on, Y/N. There's no time."

Y/N then went inside the vehicle next to Shadow as he started driving. He activate the missile and shoot off the fire monsters.

"Since when do you drive?! I have never seen you drive before! And how do you even know how to turn on the missiles?!"

Y/N was speechless. Shadow chuckled at the look on her face.

"There's plenty of more that you don't know about me. I'd rather keep it that way. Did I also mention I ride a motorcycle, too?"

"What?!"

Shadow smiled as he brought out more missiles at the fire monsters while driving. Once they are finished, they got off the Armed Buggy and jumped over to the broken road and jumped to the other up high. Shadow and Y/N fought more fire creatures as they together took down the big one with their power as they jumped up to the next platform until they made it to the giant fire tornado as they landed on the pipes and slide them. As they were sliding, Y/N looked at the tornado.

"How big is this fire?"

"No idea."

Shadow and Y/N jumped and landed onto the next pipe as they slide. Y/N did some backflip, impressing Shadow. They then got off the pipe and took down a few more fire creatures and flew up high from jumping to the building left and right. They landed on the next building filled with old glass windows and slide down and eventually made it to their stop, meeting Rouge.

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

Sonic, Tails, and Knuckles wonder about in a corridor of a ruined building.

"No matter where we go, all we see are ruins. How can this be our future?" Knuckles said.

The trio turned to look at their surroundings.

"How could it come to this?" Tails asked.

Sonic notices gas flowing from a room that is slightly opened with various notices and warnings on the door. The trio then turn to have a peak to discover what's happening. Mephiles (under Shadow's appearance), Silver, and Blaze can be seen standing in front of a large database computer.

"Could it be true?" Silver asked. "If I eliminate that guy, will our world be saved?"

Mephiles nods.

"The Day of Disaster... Here are my records of this event. This was when Iblis was freed and his flames were released into the world."

Mephiles presses a key. The screen then displayed screenshots from the present timeline.

"And you have this person to blame."

Mephiles holds his purple Chaos Emerald out. Silver takes a hold of it and stares at it. The background shifts to a stream of fire surrounding Sonic as he turns to face the camera with a stern look on his face.

"I see it! So, That blue hedgehog's the Iblis Trigger?"

"Blue hedgehog..." Blaze said.

"I'll send us back in time to the point when the Iblis Trigger was alive."

Mephiles forms an purple orb in his hands that expands, covering Silver and Blaze along with him and then disappeared out of sight. Sonic, Tails, and Knuckles approach towards the computer.

"What the... Who was that guy? He looked just like Shadow..." Knuckles asked.

"Th-This is terrible!"

Tails types on the keys.

"According to the data, the Princess died when she was kidnapped by Eggman! Apparently Eggman's battleship exploded! The date of this incident was... two days after the Festival of the Sun!"

"If we don't return in time, Elise will die onboard Eggman's battleship. That means..."

"Yeah... I think so." Tails sadly said. "Y/N's not gonna like it when hears this."

Sonic punches his hands together in frustration while Tails types on the keys.

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

Shadow, Y/N, and Rouge are walking down a street. Rouge is holding the green Chaos Emerald. Y/N was surprised that she had found it and wondered where she get it.

"My precious Chaos Emerald. You are all so beautiful. Your mysterious brilliance..."

Shadow, Y/N, and Rouge notice a dusty E-123 Omega lying down against a building.

"Omega?" Y/N asked.

"What's he doing here?" Rouge wondered.

Shadow takes a look at Omega's back display.

"It seems he's in standby mode."

"What could have possibly happened to create this future?"

"No idea, Rouge. Something's not right." Y/N said, looking at the ground in thought.

Rouge suddenly receives a message from Sonic and his friends.

"Yes, this is Rouge. Understood. We'll be there in a minute. It looks like your brother Sonic and his friends have found something, too. Let's go. It's not like we can do anything for him now."

"Yeah." Shadow said, looking at Omega.

"You're right..." Y/N sighed.

Shadow, Y/N, and Rouge walk away, Rouge a little more hesitantly.

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

At night in Flame Core, Shadow, Y/N, and Rouge meet with Sonic, Tails and Knuckles.

"You guys are so slow. Look."

Rouge shows the green Chaos Emerald.

"A Chaos Emerald! You've already found one!" Tails said in surprise.

"Well now... I may not look It, but I'm a real treasure hunter. Unlike a certain echidna I know."

"Rouge!" Y/N scolded.

Knuckles gets up in Rouge's face.

"What?"

He scoffs and walks away much to Y/N's relief.

"Have you guys discovered anything?" Shadow asked with his arms crossed.

"Um, yeah."

Tails points into the distance.

"I received a signal indicating there's a Chaos Emerald here, but..."

"You mean we've got to go through there?" Rouge asked.

Knuckles gets up in Rouge's face again.

"If you don't like it, you can stay here."

"You've got to be kidding!"

Y/N went in between Rouge and Knuckles.

"Knock it off, you two! Let's just focus on getting back home."

"You're right. Sorry, Y/N." Rouge sighed.

"Yeah, sorry.." Knuckles nodded.

"Don't be late." Sonic pointed at Shadow.

Shadow walks past him.

"Same to you."

Y/N rolled her eyes and started running ahead of them already, surprising them. Sonic, Shadow, Tails, Knuckles and Rouge soon run off after her.

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

At a volcanic pool, Rouge flies away from Sonic, Y/N, Shadow, Tails and Knuckles up to the turquoise Chaos Emerald floating in the air.

"I've found a Chaos Emerald!"

"Wait, Rouge!" Y/N shouted.

"Don't touch it!" Shadow shouted.

Iblis springs out of the lava. Rouge flies back to the group. Iblis looms over them as lava and flames boil around him

"What? What's this?"

Iblis swings at the group, hissing and snarling viciously. It jumps and dives into the lava. Iblis surface up and snarl at them again.

"Leave this to us!" Sonic said with Y/N standing beside him.

"You go left! I go right!" Y/N ordered.

"On it!"

Sonic and Y/N jumped over the rocky platform without falling into the lava as they went their separate direction as more spikes fall down into the lava, creating more platform for them to cross as they made it to where there are strange purple orbs full of energy. Iblis looked both the hedgehogs of who to attack until it decided to attack Sonic as it jumped up high. Iblis dived down to eat Sonic, but he jumped up right on time as it hit the platform and got hit in the face from Sonic's spin dash. It roared and jumped back down into the lava as Sonic flew off back into the platform as Y/N was next. Iblis turned to see Y/N still standing there as she gave it a funny face.

"Come get me, lava monster!"

Iblis snarled at her and dived back down into the lava and jumped up high, diving down to Y/N. Y/N quickly jumped as it hit the platform once again and Y/N stabbed its head with her katana. It roared again in pain, causing Y/N to fly off back to where Sonic is. Sonic and Y/N runs and skates together to the middle as they waited. Iblis charged them again after diving in and out of the lava as they both hit Iblis again but harder from spin dash and katana. Iblis roared again, feeling weak.

"Hey, what's wrong? Is that size just for show?" Sonic teased.

Sonic and Y/N landed safely as Iblis got back up, looking angry. It started throwing fire balls at them which they easily dodged them. Iblis roared at them again and started swimming towards them.

"Sonic! Y/N! It's coming!" Tails warned.

Sonic and Y/N moved to each platform to avoid being hit as it crashed into all platforms.

"It's dazed from the impacts!" Knuckles said. "Now's your chance, Sonic and Y/N!"

"On it!" Y/N said.

Together, Sonic and Y/N jumped towards Iblis and kicked it. Iblis gave a last pained roar as it was thrown backwards back into the lava. After defeating Iblis, Sonic, Y/N, Tails, Knuckles, Shadow and Rouge gathered together. Sonic and Shadow pull out the green and cyan Chaos Emerald as Y/N brought out her crystal necklace as it glowed very bright. They nod at each other as Sonic and Shadow crosses the Emeralds and Y/N places her crystal in the middle of the Emeralds.

"Chaos Control!!!"

The Chaos Emeralds and the crystal begin flashing rapidly and emit a white swirling light into the air that transforms into a blue swirling portal suspended in mid-air. Sonic proceeds towards the portal while Tails and Knuckles follow. Rouge flies into the air and turns to Shadow. Rouge flies to the portal while Shadow turns around, sensing something that gives him pause to return to the present with Rouge. Y/N was about to head into the portal when she noticed Shadow wasn't moving. She turned to see Shadow looking at Mephiles who has appeared behind him. Shadow follows Mephiles while the Time-Space rift closes behind him and Y/N after Rouge enters behind Team Heroes. Y/N decide to follow after him, wondering who was that guy that Shadow was going after. She'll explain to her brother later as she had Mephiles to deal with.