Y/N was reading a book with Kirby reading a comic when Sonic came in with a not so happy look.

"Tommy! You can't just borrow my guitar and then jet, dude. Where is he?"

"Haven't seen him." Y/N said, looking up from her book.

"I don't know. Hopefully, far from here." Rotor said as he looks grumpy along with Tails.

"I've got first dibs. He 'helped' me with my latest project. See?"

Tails showed them a damaged mechanics.

"And he washed the 'dirty' Petri dishes, which destroyed any nanite research I had going on."

"Ever since he got that does of nanites in his hell, Tommy's been acting up." Sonic said.

"As if he wasn't constantly in trouble anyway."

"Yeah, but the dude saved my life. He can't be all bad."

"No, not all bad." Tails corrected, tossing away his project.

"But don't you guys think it's odd for Tommy to act that way? Surely, there's some explanation to his behavior." Y/N said, feeling like something's wrong with Tommy.

Before they could say anything, the alarm went off. They all turned to one of the monitors.

"Nicole?! What's wrong?" Sonic asked in concern.

"Nanite *KZZT!* Infection *KZZT!* Attempting *KZZT!* To purge *KZZT!*"

"Nicole!"

"Fight, Nicole!"

"You can do it!"

"You can whip those nanites any old--"

Sonic was cut off to see a robotic fist punch through the screen as it revealed Bunnie who walked in looking like she's struggling to control herself.

"—day?"

"Nicole! Ah'm so sorry!"

"Bunnie? What's wro—"

Y/N was cut off by Bunnie punching her in the face, causing her to slam against Tails as they were sent flying towards the other room. Y/N groaned in pain, rubbing her face and looked down to see Tails dizzy.

"Oh my! Sorry, Tails!"

Y/N got up and was about to help him when she saw a shadow loom over her.

Back to the lab room

"Pooteetah!!" Kirby exclaimed for Y/N.

"Y/N, Tails, no! Knuckles! Mighty! Somebody! Get in here an' stop me!!!" Bunnie cried out.

Knuckles, Mighty, and Vector quickly ran into the room and restrain Bunnie.

"Sorry to be rough, Bunnie!" Vector apologized.

"Just stop me!!!"

Rotor ran over with the screwdriver and started unscrewing Bunnie's left arm and legs.

"It's probably the nanites! I'm going to disengage your limbs until you're cured."

"That's fine. Just keep me from hurtin' anyone or anything else!"

Bunnie's limbs stopped moving as she sat up, crying.

"Don't worry, Bunnie. Tails and I will get you and Nicole disinfected and repaired in no time!"

"Ah know. *sniff* But how did we get infected in the first place?"

"And while we're at it, where are sis and Tails?"

"Ah... Ah think ah threw them outside..."

Sonic, Knuckles, and Vector look inside the room and gasped.

"Oh no...!"

They saw Jules carrying the unconscious Tails and Y/N who looks like she's going to cry.

"Dad! No!"

"I'm sorry, Sonic and Y/N. I can't control anything but my thoughts. It's a struggle to even speak to you two."

"We need to do something..." Vector said.

"Do you want to fight Sonic's and Y/N's dad?" Knuckles pointed out.

"Leave everything to me, guys." Sonic said. "This just got way past personal."

"Pooteetah?" Kirby asked in worry, walking towards Y/N.

"No. Stay put. It's too risky. I'll be okay, Kirby."

Kirby sniffed and nodded as Jules began to run out of the Freedom HQ with Tails and Y/N with Sonic behind following him.

"Don't follow me too closely, Sonic. I don't want to lead you into a trap."

"Any idea where we're going, dad?"

"I—I— am not allowed to say, but you've been there before."

He turned to his daughter.

"I'm sorry that I have to put you in danger, Y/N."

"It's okay, dad. I trust you."

Jules look like he's about to cry from hearing that.

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

They made it to the Nanite City as Sonic had to stay hidden while Jules walk towards Eggman and a big silver turtle robot called A.D.A.M. Y/N gasped to see Shadow being picked up by the foot and carried to the machine and placed in one of the capsules.

"I'M SURE YOU WOULD FIGURE OUT MY PLAN EVENTUALLY, FATHER, BUT I DO NOT HAVE THE TIME. ALLOW ME TO EXPLAIN IT TO YOU. WITH YOUR TECHNOLOGY, I DISCOVERED THAT THERE ARE SEVEN COLORED VARIETIES OF CHAOS EMERALDS THROUGHOUT ALL THE COSMOS. JUST THINK OF ALL THOSE MAGICAL GEMSTONES WITH THEIR UNLIMITED POWER. KEEP THAT IN MIND. FOR MY PLAN TO WORK, I NEED THREE SPECIAL MOBIANS. I NEED SUPER-SHADOW FOR HIS SUPER POWERFUL CHAOS CONTROL. AND I NEED TURBO TAILS, THE CHOSEN ONE."

Jules handed A.D.A.M. Tails first as he carried him in bridal style and placed him in the second capsule.

"YES, FATHER, THE CHOSEN ONE. BEFORE I TOOK MAMMOTH MOGUL'S CHAOS EMERALD, I HAD HIM TELL ME OF THE GREAT PROPHECY. TAILS IS FORETOLD TO LEAD THE GATHERING OF ALL THE CHAOS EMERALDS AND TO BRING ABOUT THE GREAT HARMONY."

Jules then sadly handed Y/N who struggled to get out of his grip. Jules tried to get a grip of his daughter, not wanting to let her go, but A.D.A.M. roughly grabbed Y/N from him as she tried to punch him off.

"LASTLY, I NEED Y/N WHO CAN POSSESS BOTH THE CRYSTAL AND RUBY POWER. SHE HAS A CONNECTION WITH THE CHAOS EMERALD AS WELL AS THE MASTER EMERALD."

"Let me go!"

Her punch has no affect on him as he placed her in the last capsule. She banged on the glass to try and break out.

"DO YOU SEE IT NOW, FATHER? I BUILT THE NANITE CITY TO HIDE THIS FOCUSING SPIRE. I FREED MOGUL AND NAUGUS TO KEEP SHADOW BUSY UNTIL I NEEDED HIM. I USED TOMMY TO WEAKEN THE FREEDOM FIGHTERS AND OBTAIN TAILS AND Y/N. DO YOU SEE HOW BRILLIANT IT IS?"

Eggman looks like he's been scared for his life as he never knew that his creation would be so crazy.

"More like convoluted, if you ask me..."

"You won't get away with this. My son..."

"I KNOW—THROUGH YOU—THAT SONIC IS WITHIN THE CITY AND BEING CAUTIOUS OF A TRAP THAT DOESN'T EXIST. AND I KNOW YOU'VE REMOTELY SUMMONED YOUR EGG FLEET, FATHER. OF COURSE I KNOW. BUT THEY WILL ARRIVE TOO LATE."

The Chaos Emeralds began to glow green as it turned on the machine and the brought out a stream of light to the top of the machine. The capsules began to glow where Shadow, Tails, and Y/N were inside. Their eyes widen and it looks like they're screaming either in surprise or pain as they change into their Super Forms.

"A SHORT-CUT THROUGH ALL OF SPACE-TIME, A BEACON FOR THE GEMS, I WILL HAVE ALL THE CHAOS EMERALDS FROM THE UNIVERSE!"

Just then, thousands of Chaos Emeralds with different color that came from the different places and planets began to fly towards to the tower and float around it as it's being surrounded by seven different colored rings.

"ISN'T IT BEAUTIFUL, FATHER?" A.D.A.M. asked Eggman who look speechless with his mouth agape. "MY DEVICE IS SUMMONING EVERY GREEN CHAOS EMERALD FROM AROUND MOBIUS, THE CYAN CHAOS EMERALDS FROM THE PLANET WEEET, AND THE BLUE CHAOS EMERALDS FROM PLANET XORDA. HOW DO I KNOW ALL THIS? I AM BOUND TO THE SUMMONING SPIRE. THE EMERALDS ARE TELLING ME. THEY TELL ME THE RED CHAOS EMERALDS HAIL THROUH THORAXIA, THE PURPLE FROM THE REMAINS OF TERAGOSA 6, THE STAR THAT CONSUMED E.V.E. GOES DARK AS ITS FUEL—THE YELLOW CHAOS EMERALDS—ARE PULLED AWAY, AND THE GREY CHAOS EMERALDS LEAVE THEIR RESTING PLACES ON ARGENTUM. WITH TURBO TAILS—THE CHOASEN ONE—ACTING AS A BEACON, SUPER SHADOW'S CHAOS CONTROL POWERS SPEEDING THEM ALONG THEIR WAY, AND SUPER Y/N'S RUBY POWERS THAT CAME FROM COSMO TO BRING THEM HERE AS A GUARDIAN, I HAVE GATHERED EVERY CHAOS EMERALD IN THE UNIVERSE!"

A.D.A.M. turn around rubbing his chin.

"...ALL BUT ONE, IT SEEMS. I AM MISSING THE LARGEST OF THE GREEN CHAOS EMERALDS. WHERE IS THE MASTER EMERALD?"

"A.D.A.M.!"

"WE WERE WONDERING WHEN YOU'D SHOW UP."

Sonic spin dashed him who blocked his attack.

"Yeah, that's what I get for taking it slow and cautious for once. 'We?'"

"TOMMY IS STILL ALIVE AND CONSCIOUS, SONIC. HE IS COMPLETELY UNDER MY CONTROL—JUST LIKE BUNNIE, NICOLE, AND JULES WERE."

Sonic ducked the robot claw that A.D.A.M. was about strike him with.

"It figures Dr. Eggman's 'son' would go all world-conquest-crazy with the nanites."

"I AM FULFILLING MY FUNCTION. ONCE I AM FINISHED, FATHER WILL BE SO VERY PROUD OF ME."

"You're no son of mine, you digital double-crosser!" Eggman shouted, pointing at him. "I'll be happier when Sonic tears you apart!"

"SUCH SENTIMENTS ARE WHY I TRICKED YOU INTO DESTROYING M. YOU WILL LOVE ME BEST, FATHER."

"Oh, for the love of... Shadow isn't this angsty!"

Sonic managed to kick A.D.A.M. straight in the face, causing him to get dizzy.

"Time to wrap this..."

He stopped to see the face of Tommy.

"...up. Tommy, dude! I'm sorry! It's just that... UNHF!!!"

Sonic was punched away.

"YOU COULD NEVER HURT TOMMY. THAT IS WHY YOU CANNOT STOP ME."

"...Woogah..."

Eggman helped Sonic up surprisingly.

"Keep him busy for a few minutes more, Sonic. My Egg Fleet is en route, and its firepower will be able to..."

"I'm not losing Tommy. I just need to take it up a notch."

Sonic charged at A.D.A.M. who activate the rocket behind his back.

"THIS COULD TAKE A TURN FOR THE WORSE VERY EASILY. I MUST TAKE MORE DRASTIC MEASURES."

They ran or fly up to the top of the machine.

"Copy-turtle! Or robot or cyborg. Whatever."

"DO YOU EVER SHUT UP?"

Once they made it to the top, Sonic turned into Super Sonic.

"Whoo-ha!!! Come on out, A.D.A.M.! I'm ready to rip every last Nanite of you off my friend!"

"IF YOU INSIST."

A.D.A.M. also turned super as he has golden wings. This will be difficult.

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

Eggman opened the three capsules, freeing Shadow first.

"Wake up!"

Then, Tails.

"Get out!"

And lastly, Y/N.

"Snap out of it, Y/N!"

They slowly stood up as they're still in their Super Form.

"A.D.A.M. has gained super-level power! Super Sonic can't take him alone, much less my Egg Fleet! You three have to do something!" Eggman said, pointing at the green explosion as Super Sonic and Super A.D.A.M. fought in the air.

Y/N nodded.

"We'll do our best."

"Yes..." Tails agreed. "I know what must be done. Super Shadow, will you please help us?"

"Of course."

"What do you have in mind, Tails?"

Super Shadow, Super Tails, and Super Y/N flew up to the top of the machine.

"That much power cannot exist here, we must send it to a safe place. Can you open a portal to the nearest zone? Not another dimension, entirely, but..."

"I understand, Chaos Control!"

Shadow created a portal as his hands glowed so powerful.

"The Zone of Silence." Y/N said in realization.

"Why do we always end up with the Zone of Silence?" Tails sighed. "Y/N. Once we bring all the Chaos Emeralds into the portal..."

"I got it."

Y/N summoned her bow as she pulled the string with lots of arrows as she could bring out.

"This isn't easy. What's next?" Shadow asked.

"I fulfill the prophecy I thought I'd already finished. This is the beginning of the great harmony. Where all the Chaos Emeralds are unified!"

Tails' hands glowed as they made all the Chaos Emeralds fly into the portal of the Zone of Silence.

"What will happen with all that energy in such an unstable zone?"

"Something special, I hope."

Once every last bit of the Chaos Emeralds are send into the portal, Y/N let the arrows go as it shoot into the portal and make the portal close with a giant shining star that blinks before it disappears. Super Shadow, Super Tails, and Super Y/N landed next to Eggman. Y/N looked up to see Super Shadow and Super A.D.A.M. still fighting when she saw a face of Tommy come out from A.D.A.M.'s face. Y/N gasped to see him as she could hear the conversation between them.

"Hey, Sonic."

"Tommy? Is it really you this time?"

"I'm sorry it took so long to win back control." Tommy looked away in shame. "I'm sorry for everything, really. I'm sorry I've been such a pain. I'm sorry for all the trouble I've dragged you and Y/N into. And I'm especially sorry for letting A.D.A.M. do this to everyone."

"Dude, it's cool. You're in control now." Sonic assured him with a smile.

"No, I'm not. A.D.A.M. will win back control any minute now, and I won't be able to get it back. A.D.A.M. must be destroyed so that everyone will be cured of their nanite infections. I'm sorry, Sonic... You and Y/N gave me a second chance in life. It's time I repaid that debt!"

Tommy flew up to the Egg Fleet that are waiting for Eggman's command.

"Tommy!!!! No!!!" Sonic shouted.

"No..." Y/N covered her mouth, feeling tears spilling down her cheeks.

"Dr. Eggman to Egg Fleet! All cannons— FIRE!"

"TOMMY!!!"

All Egg Fleet blasted at Tommy/A.D.A.M. destroying him as his body turn into smoke. Y/N and Tails began to cry at Tommy's sacrifice. Shadow stayed silent as he placed a hand on her shoulder to comfort her.

"So much for family. What a colossal waste of time and I missed out on a literal ton of Chaos Emeralds. Come along, Shadow... We're done now."

Shadow was hesitant for a sec before he release himself from Y/N as he followed Eggman whilst looking back at her in sympathy. Sonic landed on the ground as he, Y/N, Tails, and Shadow are no longer in their super form.

"I'm letting you go for now, Sonic and Y/N." Eggman said with a wave. "I've had too long of a day to deal with you two right now."

"...Sure..."

"Tommy..." Tails whimpered, hugging Y/N who sniffed.

"...was maybe the bravest Freedom Fighter of us all. And he took A.D.A.M with him." Sonic finished his sentence, staring at the pile ash of Tommy in his hand as it flies away.

He placed a hand on Y/N's shoulder as she wrapped Sonic and Tails around their waist to hug them.

"C'mon, guys. We need to get my dad home."

"Right..." Y/N nodded, wiping away her tears that won't stop falling.

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

Y/N is right now walking through the Great Forest as she wanted to be alone for a while through the night. Kirby had to stay in the treehouse as he wait for her return while worried for her ever since Tommy's death. It seems that everyone she knows ended up gone. Who will be next? Her parents? Her... She shook her head, not wanting to think about it. Y/N looked up at the moon with a sigh as she's now near the clear lake that sparkles. She sat down, staring at the reflection of herself. Y/N closed her eyes as she began to sing to distract herself.

As she sings, she didn't notice she caught the attention of someone which happen to be Fiona that came back from who knows where as she's up to something. Fiona heard her singing voice and followed it and found Y/N sitting there. She may or may not heard what happen to Tommy and felt bad for hearing that. She lean against the tree to listen throughout the night.

Y/N could feel everyone's pain as they're thinking about their loved ones they cared for deeply. She wished she could go back in time to save them, but she can't. Things happen and it has to be this way. Sometimes the world can be cruel. She knows she has to keep moving forward, knowing they are still there watching over them.

As soon as she finished singing, Y/N lie down on the grassy ground and look up at the stars. Fiona suddenly felt a tear from her eye and wiped it off. She want to tell Y/N something, but she can't. She thinks that there's a path that will help her guide her to her old days.

The snores was heard and Fiona turned to see Y/N softly sleeping. She couldn't believe she's sleeping at a time like this when it's cold and dark outside. She walk over to her and carried her in bridal style. Fiona looked around for a place she might be living as she walk through the forest. Y/N snuggled into her chest, thinking it's her blanket, causing Fiona to blush. Fiona then found a treehouse and knocked on the door. The door opened to reveal Kirby who's surprised to see her until his eyes set on Y/N. Kirby shook his head and pointed at the room. Fiona was surprised that he didn't question her on where she had been off to lately and then guided Y/N to her bedroom. She took off her shoes first before placing her on the bed and tucked her in a blanket. Fiona smile down at the sleeping Y/N and kissed her on the head. Kirby jumped on the bed next to Y/N and fell asleep after.

Fiona chuckled and turned off the lights for them and left the treehouse after as she closed the door softly. She looked back at the treehouse one more time and walked away quietly.

"Be better, Y/N."