(A/N. Here is part one of that AU thing. Warning: It's gonna get a little creepy and weird. You'll see what I mean.)

Rumors of Team Rocket's uprising had been circling Kanto and Johto for weeks. The citizens of both regions have been looking to their champion for guidance, but Lyra had no idea what was going on. She had demolished Team Rocket and sent Giovanni to jail years ago. Without their charismatic leader, Team Rocket should not have been able to function.

Lyra's Typhlosion sat at her feet, his head in her lap. She stroked her Pokémon's muzzle, scratching his warm fur. Lyra's Elite Four sat around her, along with her sixteen gym leaders and three other trainers.

"What are we supposed to do?" Misty asked, "These grunts are coming at us hard. I can't even imagine how strong the admins are, let alone their leader!"

"Lyra sent Giovanni and his crew to jail ten years ago," Blue said, "How are they active again?"

"Well Giovanni wasn't technically involved the second time, right?" Gold asked, "Maybe it's just some grunts uprising?"

"Perhaps Giovanni is running things from prison?" Koga suggested.

Lance frowned, "Wouldn't that be difficult? Isn't he completely cut off from other prisoners?"

Morty yawned, "Who cares? What's important is we've taken them down twice before!"

"Have you seen these grunts?" Jasmine asked, shuddering, "There's something going on. They're really strong. They make me look like a rookie."

"Ariana's sentence wasn't as long as Giovanni's. She's his wife, right? Maybe she's running the ship?" Blue suggested.

"I think it's time we acknowledge the most likely scenario," Red said quietly, gaining the attention of everyone in the room, "There's only one person with deep connection to Team Rocket that didn't go to jail- The only other person the grunts would take orders from."

Lyra glared at Red, "Don't say it."

Red stared back at Lyra, "Silver."

Lyra chuckled darkly, "Silver hated Team Rocket."

"Under his father's management. Maybe he thought he could do better."

"He wouldn't!"

"Lyra," Gold interjected, "You haven't seen Silver in ten years. You don't know him."

Those eyes. Those silver eyes she thought of non stop for the past ten years. Silver would never do this. He was lost, scared, and angry when she met him. He hated Team Rocket.

Though...Silver did pull away when Lyra offered him friendship. She offered him a new path, but he ran away. The last time she saw those silver eyes, they were full of panic and fear. She never saw him again, but she knew there was no way he could be capable of evil. No way in Hell.

Lyra shook her head, "You're wrong. We'll find their new hideout and I'll prove it!"

All the trainers in the room exchanged nervous glances. Lyra adjourned the meeting and nearly everyone exited the room. Red, Blue, and Gold hung back.

Gold put a hand on Lyra's shoulder, "You know we'll help you, Lyra," he said calmly, "But...You have to be open to the possibility that you may not see what you want at the end of the line."

Lyra pulled away from Gold and stood up. Typhlosion pulled away from his trainer's lap. Lyra nodded solemnly and retreated into the Champion's Chambers. Typhlosion sighed, smoke flowing from his nostrils.

"I don't think this is a good idea..." Blue sighed.

Red nodded silently. Typhlosion finally followed his trainer, and the three men left the way they came in.

~~~

"Faster!" Lyra cried, hanging on tight to her Dragonite, "Hurry!"

Dragonite grunted and sped up her pace, flying swiftly towards the smoke plumes. Dragonite stopped dead in her tracks as they reached the source of the flames. Lyra gasped.

Ecruteak City was on fire. The gym, the dance theatre, the houses, the Pokémon Center- everything- was burning to the ground. All that remained of Burned Tower was a pile of ash. Bellchime Trail and Bell Tower were both encased in flames.

Dragonite spotted a party of Pokémon shooting flames from their mouths. She sped towards them, using a Surf attack to douse the Pokémon and their flames.

Lyra's feet hit the ground, getting surrounded by the party of now angry and wet Charizards and Typhlosions. Dragonite landed near Lyra, ready to attack once more. Lyra sent out her Rhydon, who was ready to assist Dragonite in the takedown of the fire type army.

A set of fingers snapped. The fire type Pokémon stood down and allowed a tall figure through to Lyra. They smirked and stared down at the Champion. Lyra's Pokemon growled and bared their teeth.

"Oh, put those away," They hummed, "They won't be necessary."

"Ariana," Lyra hissed, "I should've known you were behind all of this!"

Ariana's smirk grew smugger, "The Lake of Rage."

Lyra frowned.

Ariana threw a Pokéball into the air and turned around to walk away, "Our boss is waiting for you. He is not a patient man."

The fire types retreated with Ariana as a Blastoise appeared from the Pokéball. It immediately fired shots of water into the atmosphere, causing it to begin raining heavily. The fires around the city became suffocated from the rain, and Blastoise walked away.

Lyra and her Pokémon stood still in shared confusion. Rhydon cringed from the rain, and Dragonite extended a wing over her friend.

Lyra's pigtails drooped from the heavy rain. She shook her head and addressed her Pokémon, "We're going to the Lake of Rage."

Both Pokémon nodded and Lyra returned Rhydon to her Pokéball. Lyra took out her Pokégear as she climbed onto Dragonite's back. She called Gold, Red, and Blue on the way to the Lake of Rage. She knew they were going to be close behind her.

As she reached the lake, she saw nothing out of the ordinary. As she stepped off of Dragonite's back, the lake's red Gyarados greeted Lyra happily. Lyra chuckled as the Pokémon nuzzled her.

Lyra frowned and looked around, "Where is this hideout?"

Gyarados nudged Lyra gently and swam into the lake. When Lyra didn't follow, Gyarados appeared again.

"It's...underwater?" Lyra asked.

Gyarados nodded and swam away. Lyra took a deep breath. She returned Dragonite and sent out Togekiss.

"Psychic." Lyra commanded.

Togekiss smiled and used Psychic on the water. Togekiss pulled the water apart to reveal an entrance on the lake's floor. Lyra and Togekiss rushed over to the entrance and opened it. The two of them dropped inside before Togekiss's attack wore off.

Lyra and Togekiss found themselves in a long, dark hallway. Togekiss whimpered and cuddled close to Lyra. Lyra smiled gently and stroked the Pokémon's feathers. He might be ten years old, but Togekiss was still the team's baby. Sometimes he acted as if he just hatched.

There were dim orange lights along the walls, barely illuminating the floor. Lyra gulped and began walking down the long hallway. She could hardly believe they were underwater- How could a place like this even get built?

The hallway split in half, leading in two different directions. Lyra frowned. She moved off to the right to find an even longer looking hallway. She sighed and checked her Pokégear as she walked. There was no reception down here, so there would be no contacting her friends in an emergency. Togekiss nudged his face under Lyra's hand. He could tell she was nervous.

Lyra sighed, "There's no way this place is empty. We'll probably have to fight our way through. Be on your guard."

Togekiss nodded.

Reaching the end of the hallway, Lyra found a door. Taking a deep breath, she pushed the door open. She found herself surrounded by Team Rocket grunts. They seemed to be waiting for her. A Gengar, Alakazam, Donphan, Scizor, and Nidoqueen stood near their responding grunts, ready to fight.

Lyra gulped and held her head high, "Ready?" She asked.

Togekiss nodded, "Toge!" He chirped.

The grunts attacked.

~~~

Lyra and her Pokémon pushed through the rooms of the Team Rocket hideout. Each room and grunt seemed more difficult to defeat than the last, and her Pokémon were paying the price. Typhlosion was the only one running with any gas, and that was not good. There was no telling how many more grunts there would be. Typhlosion may be up, but he was tired and injured. Lyra had run out of medicine three battles ago. She couldn't turn back, however. Her only hope was getting to the leader and stall enough for her friends to arrive.

Lyra burst through a large metal door and came upon a large, empty room. Four doors on the side walls slid open, and four Houndoom appeared from them, growling and barking. Typhlosion sized them up, deciding he could probably take them. One more door slid open and a large Feraligatr charged at Typhlosion. The two Pokémon wrestled for a bit, but the water type pinned Typhlosion down, readying a Hydro Pump attack. Feraligatr held the attack as one more figure entered the room behind Lyra.

"Finally, you're here." A voice said.

She didn't recognize the voice, but tears slipped down her face. She knew the Feraligatr. She knew exactly who was behind her. This was Lyra's worst fear.

"Didn't you miss me?" They whispered, leaning into Lyra's ear.

"Silver..." Lyra gasped.

Silver chuckled and stepped in front of Lyra. He wiped Lyra's tears, "Hey."

Lyra pulled away. Silver frowned, "Oh don't be like that..." he hummed, "Don't make this hard..."

Lyra wiped her eyes with her sleeve, "Call off your Feraligatr!"

Silver rolled his eyes, "Oh Lyra," he sighed, "I can't do that."

"Why are you doing this? You hated Team Rocket!"

Silver raised his eyebrows, "My father ran this organization horribly. Grunts were poorly equipped, without leadership, and quite simply, utterly useless. I decided to equip grunts with stronger Pokémon, and I trained more admins. It's impressive, no?"

"No." Lyra spat.

Silver smirked, "It got your attention, didn't it?"

"You burned down a whole city! For what? My attention?"

"Exactly."

Lyra paused, "W-What?"

Silver smirked and took Lyra's chin in his hand. He had her look up at him, "I've thought of nothing but you these past ten years. I've thought of nothing but this moment."

Lyra blushed. A devilish look found its way into Silver's eyes, "I can tell you've thought of me, too."

Lyra scowled, "I haven't." she lied.

Silver's expression became blank and he grabbed the sides of Lyra's face gently, "You will."

He walked away from Lyra and snapped his fingers. Feraligatr got off of Typhlosion and rushed to Silver's side. The Houndoom exited the way they came in.

Silver looked over his shoulder at Lyra, "Your friends are here for you, but don't worry- You'll see me soon," He turned his back to her and began walking away, "If you come to Ilex Forest tomorrow night, I'll reward you. Come alone."

The doors in the room all slammed at once. Lyra let out a breath she didn't know she was holding and rushed over to Typhlosion.

"Are you okay?" She asked, stroking her Pokémon's worryingly cold fur.

Typhlosion grunted and closed his eyes. His chest rose up and down hurriedly, and Lyra could tell me was in immense pain. Just then, Red burst through the door. He noticed Lyra and Typhlosion and rushed over to treat the Pokémon immediately.

"You were right," Lyra sniffled, "It's Silver."

Red frowned and placed a hand on Lyra's shoulder. Once Typhlosion was stable, Red ushered Lyra and her Pokémon out of the hideout. No grunts stood in their way this time- they just simply watched them leave.

The two trainers met up with Blue and Gold closer to the entrance, and Lyra fell into Gold's arms.

"My Silvey can't be gone..." She whispered.

Gold sighed and stroked Lyra's hair. He and the other boys escorted her out of the hideout and back to her home. She needed her rest. They knew the real battle was just beginning.

~~~

Lyra couldn't sleep most of that night. She woke up all hot and bothered from a dream about Silver. She groaned audibly, waking up the Bellossom sleeping in the flower bed on the windowsill. Bellossom gave Lyra a worried glance.

"Go back to sleep- I'm fine." Lyra whispered.

Bellossom yawned and snuggled back into the flowers.

Lyra stared up at the dark ceiling. How dare he? Seriously, how dare Silver ghost her for ten years and suddenly appear again? How dare he attack cities, people, and Pokémon just for her attention? How dare he make her feel...like this? He had no right.

I can tell you've thought of me, too

I haven't

You will

Lyra blushed.

Stop it! That's disgusting! She thought.

But it's Silver

Lyra threw her pillow over her head and attempted to go back to sleep. She eventually drifted off, thoughts of Silver still plaguing her mind.

She spent the next day as normal- a shower, breakfast with the Elite Four, a bit of training, and then challenges. She didn't have many today- a lot of them couldn't seem to get past Bruno. Lyra and her Pokémon demolished every challenger that did manage to make it to her, continuing to keep her Champion status.

After she and her Pokémon had lunch, Lyra took a nap. She wanted to regain the sleep she missed. It was dinner time by the time she woke up, and everyone made fun of her for it. They told her she had a few challenges to make up tomorrow, but she didn't mind. She had a Silver-less sleep.

After she and her Pokémon ate, she went back to her quarters and changed. She put her brown hair into pigtails, wore a pastel yellow long sleeved shirt, and put on a pair of overalls. She grabbed her bag and left the league.

I can't go, She thought, Why am I going?

Meeting the leader of Team Rocket in Ilex Forest was probably not a great idea. Meeting him alone in Ilex Forest was definitely a bad idea. Regardless, Lyra trudged on, holding on to some hope that Silver was still the kind soul she once knew.

Twigs and leaves crunched underneath Lyra's feet. Where was she even going? Where would Silver even be?

Lyra reaches the Ilex Forest shrine. She smiled softly and ran her fingers over the foliage that was growing over it. She met so many precious Pokémon friends here...but that was a long time ago now.

"I'm glad you decided to meet me."

A shiver went down Lyra's spine. She turned around to find Silver and his Feraligatr a few feet from her.

Silver cocked his head slightly, "You didn't come alone." He said, staring at Lyra's bag. He must've known that's where she keeps her Pokéballs.

Lyra frowned, "Neither did you."

Silver nodded, "Fair enough," he hummed, "Hello, Lyra."

Lyra blushed and looked away, "Hi."

Silver made a gesture to his Feraligatr, and the Pokémon walked away into the forest. Silver smirked, "So, why has the champion decided to grace me with her presence? To what do I owe the pleasure?"

"You asked me to come?"

"Here for your reward?" Silver asked, smiling devilishly.

Lyra blushed, "What could you possibly have that I want?"

Silver thought for a moment, "...Did you shower this morning?"

Lyra looked confused, "Yeah?"

Silver smiled and bit his lip, "Ah..."

"Why?"

"I just...I thought you were a night showerer."

"So?" Lyra asked, raising an eyebrow.

"You asked what I have that you could possibly want," Silver said, stepping closer to Lyra. He leaned his face in towards hers, "I think you want me..."

Lyra blushed and turned her face to the side, "Yeah right!"

Silver smirked, "You're blushing, refusing to make eye contact with me, and you showered in the morning when you're very public about showering at night."

"I was sweating..." Lyra mumbled.

"From what?" Silver whispered challengingly.

"You're disgusting!"

"I prefer the term 'observant', Pigtails," Silver hummed, gently touching one of Lyra's pigtails, "Speaking of...You haven't worn your hair like this in years...I'm flattered you saved the occasion for me."

"What do you want?" Lyra asked.

What was the point of this? Of any of it?

"I want you," Silver said, as if it was obvious, "I want you to be with me."

Lyra bit her lip. She felt like crying, screaming, and punching Silver in the throat. She also felt like doing whatever he wanted, but she pushed that down.

"Well? Tell me what you want." Silver growled, putting his hands on the shrine and boxing Lyra in.

Lyra looked up into the set of sharp silver eyes in front of her, "I want my sweet Silvey back..."

Silver scrunched up his nose, "You came all this way for him?"

Lyra nodded.

Silver removed his hands from the shrine and stood up straight. He glared down at Lyra, "He's gone."

Lyra sighed and looked away, "Then I guess we're done here."

Silver sighed, "I suppose so..."

He turned and walked a few steps away, "You and your friends best be on your guard. Don't say I didn't warn you."

Feraligatr rejoined his trainer, and they walked through the forest together. Lyra took a deep breath and fell to the ground. She couldn't help but cry. She couldn't believe the face of her childhood love was now the face of her enemy.

How was she supposed to believe he was completely evil? He couldn't be like his father.

Could he?