DWA: What's up!? Not much to say, I don't really wanna spoil anything ya know? I'm just glad people are enjoying the energetic Lily as much as I enjoy writing her! I'll keep this short but will say that her original team has changed, I can't say one because people may either protest etc but it helps the spacing. But one was a Zorua found in Goldenrod. This was planned for a long time but was replaced as I did make the restriction of Johto only for others, why not restrict the same to myself? So I got rid of the Zorua in favor of a more um, useful, Pokemon. On to reviews.
I own the plot and my OC's, RedAgent14 and KnightofStories own their yet to appear OC's

Reviews:

RedAgent14: They uh, have had Whitney for some time now. She just joined on her own. I didn't even have a reason I chose looked at the gym leaders and said wouldn't it be funny if Whitney was evil.
Then I discovered people hated her and I was like "uh…I swear I don't hate her."

Xenexis: Yeah Lily is gonna be pretty hyper and probably destroy her sleep schedule. Lily may be new, but she knows not many first route Pokémon have long standing strength. She'll deal with her team as any normal trainer, switching out Pokemon from time to time, keeping a select few with her at all times.
Also, Giritina isn't uh, planning anything. All he marked her for was the rescue of Lugia. Giritina isn't evil, and cares for Lugia as he went through the process of becoming a Shadow Pokémon. Ah, Lugia did, not Giritina.

TheAdmirable402: Alex is special. Wearing a hood and mask as well as gloves, there is nothing about the mans features that's known besides his humanity and his red hair. In truth, no admin in ES trusts Alex in full, even David is cautious. Alex has an unnatural distance from the consequences of murder psychologically, seeing as he put a bomb in a school without a second thought. David is by no means a savage, but neither is Alex, far from it. Think of a Cyrus from Team Galatcic, but missing all the "right" emotions, like regret.

TeslaThePikachu: Knowing Alex, secretive and brutally

Wow those lasted. Guess I had explaining I wanted to do, wrongs made right and all.

"Speech"

'Thought'

[Translated Pokespeech]

Chapter 3: Violet City

-(o)- 11:29 pm

Alex stood on top of the factory, far from any civilization. It was perfect. A huge beast stood beside him.

"Shadow Lugia, I want two things right now. Team Rocket is getting supplies from Kanto via plane. I want to test your might, and that plane stopped." He said. He was very happy he was lent this powerful creature from David. He didn't plan to use its power much, best not raise suspicion. "I don't want a 40 day storm. A day is all I need." He said. "Go."

The beast silently took off in the sky and stopped in place and roared, storm clouds forming fast and spreading far. It soon started to rain and the wind kicked up and howled. Alex started laughing.

"Yes! Yes!" He shouted. This will delay them, we can call on the storms whenever we wish!" He shouted. "I will be sure to make use of this." He said and returned the Pokémon when it started flying back. He walked inside, dripping wet. He pulled a part of his jacket to his mask.

"No one go outside, we have quite the storm on our hands." He said and his voice could be heard inside. 'This can cover our more, discreet operations.' He thought as he walked to his office

-(o)-

Lily and Midnight had made it far through the short route quickly, and the lights of Violet City were near.

"Almost there!" Lily said happily. "Then we can sleep." She said

[I long await for that.] Midnight said smiling. She was tired yes but pushing through for Lily.

"So…what do you think the Gym Leader has?" Lily asked

[I'm not sure…maybe-] She started but stopped. Lily looked at Midnight as she looked into the distance.

"Midnight?" She asked.

[Run.] She said

"Huh?"

[RUN!] She said and knocked Lily on her back and took off at full speed. Lily, confused at her action looked in the direction she was before running and saw massive storm clouds racing towards them.

"What the hell!?" She shouted. Sher normally watches her language but storms don't form like that. "Agility!" She shouted and Midnight picked up the pace. There was a trainer walking along the path up ahead. "HEY! STORM COMING!" She shouted as they raced by, she hoped the trainer would heed her warning. Her Holo caster started beeping

"This is a Johto Weather Warning Forecast, a powerful storm has broken out and is spreading to major cities like Violet City, Goldenrod City, Azalea Town, and Ecruteak City. Citizens are advised to seek shelter wherever they can." The announcement said.

"Four cities!?" She shouted nearing the gate, many trainers were running in.

[We have to get to the Pokémon Center!] Midnight said and blazed through the checkpoint and into the city. As soon as they got outside the storm washed over the city, the winds were harsh and the rain was cold.

"I can't see it here! Head for that large tower!" She shouted over the winds and she looked back to see officials preventing trainers from leaving the checkpoint. Midnight took off towards the tower and quickly reached it. Lily hopped off and banged on the door. The wind was really harsh. The door opened to a surprised man.

"A young lady, please come in out of this terrible storm!" He said and let Lily and her Absol in. As Midnight shook the water off away from everyone Lily shivered.

"Let me get you a towel, you should change over in that room." He said and walked off. Lily walked over to the room and Midnight stood guard.

"Thank you so much Midnight. Without you I'd be in that storm with nowhere to go." She said and came out in simple PJ's. The monk came out and handed her a towel and she tried her hair. "Thank you so much sir." She said

"In a storm such as this I would never turn away anyone from here. Just be careful, wild Pokémon have their home here, and generally play, or rather, battle newcomers." He said and Lily nodded.

"Can I sleep in that room?" She asked.

"Of course, rest all you need to." He said with a warm smile. Lily nodded and went back in the room with Midnight. Lily was setting up her sleeping bag.

[I don't get this storm.] Midnight said. [It just…appeared.]

"It'll be okay." She said and snuggled in her bag as Midnight sat by her.

[Don't get sick.] She said to Lily.

"I won't silly." She said and sighed and closed her eyes. The door closed after the lights turned off. The monks were offering others sanctuary from the terrible storm outside.

The other cities were having the same issues, luckily Pokémon Centers, Gyms and other such places were open for trainer and civilian use.

Lily was just hoping everyone would be okay as she slipped into sleep.

-(o)- 5:21am

Lily woke up needing a drink, and sat up and rubbed some sleep out oif her eyes. Midnight was out like a light. She grabbed Zack's Poke Ball and walked out of her room to see many trainers on the floor spread out, the storm was still raging on.

"Hey kid, bathrooms back there." One whispered with a smile. "That's my guess as to why you're up." He said.

"Thank you." She whispered back and walked through the door and started walking down the hallway, the bottom floor was much much larger than the rest of the tower's floors. It was quite a walk. She came to a window to see the storm raging. She gripped Zack's ball tight.

"This feels….unnatural." She said. She sighed and saw something out of the corner of her eye, and spun around and gasped when she saw a Pokémon. It was a black ball surrounded by a purple mist, and it had a face.

"A Gastly?" She said. The Gastly stuck out its tongue. "Oooh, you wanna play?" She asked and held up the ball. It nodded and Lily tossed her Poke Ball and her Ralt's appeared with a yawn.

"Zack, up for a quick battle?" She asked and Zack nodded. "Let's start! Double Team!" She said and Zack made copies of himself and the Gastly blew out a white smoke and washed it over the copies, all but one vanishing, Zack had been caught in the attack and was coughing.

"Confusion!" She shouted…quietly. She was trying to now wake anyone. Zack glowed pink and blew the smoke away and hit the Gatsly, causing it to cry out. It flew to Zack and…licked him, causing Zack to shiver and wipe the saliva off his face. "Confusion direct attack!" She said

Zack shot what seemed to be an orb of energy at Gastly and hit her hard. Both had super effective attacks, but Zack was much more powerful.

Gastly shot the clear smoke at Zack with a more concentrated stream and hit him, pushing him back. Zack opted on his own, another confusion, throwing Gastly into a wall, who wasn't prepared and hit it.

"Zack, Teleport to my bag and get a Poke Ball!" She said and Zack Vanished and Gastly started to get up. Zack appeared on Lily's shoulder and dropped the Poke Ball in her hand. She tossed it and it hit its mark, and sucked the Gastly in. The ball landed and shook, until it pinged, sparks coming off it. Lily smiled and walked over and picked it up.

"Welcome to the team Gastly." She said and walked on to the bathroom to finish her original mission.

To get some water.

-(o)- 9:45 am

Lily yawned as she woke up and rubbed her eyes. Midnight was already up as was Zack.

[So, something, or rather, someone, tells me you caught us a new team, member.] She said with a smile. Lily nodded. She grabbed her Holo Caster and turned it on to the news.

"The storm that has covered four cities has calmed and trainers can now resume their travels." Lily sighed happily. She then called out the Gastly she caught last night.

[Ahh, so I was captured, Oh well, not the worst thing. Hello.] The now made obvious female Gastly said to her new companions. Lily checked her stats as she thought of a name. She quickly closed the screen as she just needed to look them over.

"Gastly, do you mind being called Phantoma?" She asked

[Phantoma? Odd name but no I do not mind that being my nickname.] She said.

[Welcome to the team Phantoma.] Midnight said and Zack smiled.

[I'm Zack!] He said

[And I'm Midnight.] She said.

[Nice to meet you both.] Phantoma said

"I'm Lily, I know we'll be great friends!" She said and Phantoma smiled.

[I'm glad I got a kind trainer.] Phantoma said. Lily quickly got dressed and packed up. Her clothes had dried during the night. She walked out and wnet over to the door.

"Hey, still raining." One trainer said

"So? We're Trainers right?" She asked picking up Zack. "It's better than it was last night, so, what's a bit of rain?" She asked and left with her Pokémon. She ran through the city until she got to the Pokémon Center and walked to the counter, many trainers were lounging around.

"Nurse Joy, can you take these two?" She asked and set Zack on the counter and Phantoma floated over. The woman picked up Zack and nodded.

"Of course! Please come with me Gastly." She said and the ghost followed as Lily went to the cafeteria.

She walked in with Midnight and Lily started to get food for the two of them.

"What could have caused the storm?" Someone said

"Maybe it was a Pokémon?" Another said

"What Pokémon could do this?" Person A asked.

"Lugia?" A girl asked lazily. Lily just up and stopped, the mark on her back compelling her to before she shook her head and kept moving. She knew of her duty here set by Giritina, but that wasn't her priority.

"Possible, people say Lugia was spotted not too long ago, headed for the Whirl Islands." Lily had to at least know where these were. She finished and walked up to the group.

"Sorry but may I ask a question?" She asked. These trainers looked older than the others.

"Sure kid, what's up?" A boy asked.

"Where are the Whirl Islands?" She asked. "I'm not from here."

"Oh, between Olivine City and Cianwood City. Boats keep away so if you wanna check em out you'd need to ride a Pokémon." The girl said. "Hunting Lugia?" She asked with a laugh.

"I mean…sort of?" She asked. "I more just want to meet it." She said shrugging.

"Well give it up kid, Lugia are very secretive. They need to be summoned rather than just found." The second man said.

"Well that's not of a concern for me…I'll find it. Not now but later of course." She said smiling. "I'll be fine, I won't battle it." She said and walked off. The group shrugged and kept talking as Lily sat down with Midnight and started eating.

[Was that because of you "Master?"] She asked

"Oh hush I called him that to mess with him." She said giggling.

[Not wise.] She said

"I'm a kid." She said smiling and laughing. Midnight sighed and quickly finished her food, as did Lily. "Ready to fight the Gym?" She asked.

[As a last resort only.] She said. Lily giggled and set her tray away and went over to Nurse Joy. Phantoma was chasing around Zack, who was laughing happily.

"Guess their ready." Lily said, and Nurse Joy nodded. "Thank you very much." She said and picked up Zack and started walking, her other Pokémon following. The second they got outside they ran to the gym. They quickly found it thanks to Lily's Holo Caster and walked in and shook off the water. Many trainers were hanging out. A man came over.

"Here to seek shelter?" He asked. He had a robe and one eye was covered by hair.

"No sir, here for a gym battle, if the leader is willing." Lily said

"I see, he's willing alright." He said with a smile. "My name is Falkner, I'm the Gym Leader." He said and Lily smiled.

"Thank you sir!" She said. "I'm Lily Zenex, just call me Lily!"

"Alright Lily. Trainers! Please clear the field! I have a challenger. The trainers nodded and headed for the stands as he walked to his box and Lily to hers. "I have simple rules. Two on two, I can't substitute, first one to lose both Pokémon loses. Ready?" He asked. Lily nodded

"Of course! Go on Phantoma!" She said and the ghost nodded and floated onto the field.

"Interesting. Go, Spearow!" He shouted and he tossed a Poke Ball, it opened causing the aggressive looking bird to appear. "Take the first move!" He said and Lily smiled.

"Gladly! Clear Smog!" She shouted and Phantoma let out a stream of white smoke that slammed into Spearow, throwing it back.

"Peck!" He shouted and Spearow shot at Phantoma, flying low.

"Night Shade on the ground! Tear it up!" She shouted and Phantoma shot the attack into the ground, breaking it up as it went. Spearow flew into the rocks and dirt and had to fly off course to avoid any more damage.

"Well then." Falkner said. "Peck!" He said and Spearow started to turn.

"Clear Smog with a spin!" She shouted and Phantoma spun while blowing clear smog, and Spearow dove in, and then flew out coughing. "I think we got this Phantoma! Clear Smog! Stream it!" Phantoma let out a concentrated stream of the attack that hit Spearow dead on. When it cleared Spearow was out and Falkner recalled his Pokémon.

"One down, one to go. Pidgeotto!" he shouted and tossed a Poke Ball in the air, and the evolved bird appeared.

"Phantoma, come on back." Lily said and Phantoma floated over.

[How was I?] She asked

"Amazing Phantoma! Zack, you're on!" She said and threw the small Pokémon up and he landed and glared at his opponent

"Wing Attack!" Falkner shouted and Pidgeotto's wings glowed with power and charged at Zack.

"Ready, Teleport!" She shouted and Zack vanished and reappeared on Pidgeotto's back. "Disarming Voice!" She shouted and Zack let out a cute shout that did damage to Pidgeotto as he kept yelling.

"Shake it off!" He shouted and Pidgeotto started flying erratically to get him off, Zack held on tight even as Pidgeotto flew straight up.

"Confusion!" She shouted and both Pokemon were covered in a pink glow and Pidgeotto squawked as it struggled against the pain.

Zack's eyes shot open, as they had been closed to prevent fear from showing. He was out of view of everyone. His hand became shrouded in dark energies and slammed his fist into Pidgeotto's head hard, the bird let out a strained yelp and started to fall. Zack gasped and Teleported down and looked at his hand. He…hadn't meant to do that. He looked up and saw Pidgeotto plummeting down and used Confusion to slow it and let it touch the ground gently, unconscious.

"Wow, impressive power." Falkner said and recalled Pidgeotto." He said and Zack was picked up by Lily. Falkner walked over as trainers in the stands clapped.

"Well, here's your badge, the Zephyr Badge." He said smiling. Lily happily took the badge.

"Thank you so much sir! I wanna get moving to Azalea Town right?" She asked

"That's right. Head south and through the Ruins of Alph and you'll be pretty close. Feel free to take an umbrella." He said pointing to a large rack of them. "The League supplied them to Centers and such a long time ago, in case something like this happened." He said.

"Thank you again!" Lily said and ran over and grabbed one and smiled. "Bye bye!" She said and left the building.

"Yo Falkner, you didn't tell her those ruins can be dangerous." One trainer said

"They've been relatively safe, she may seem reckless but that Absol of hers warns her of danger I'm sure." He said smiling. "She'll be fine."

DWA: So Lily first catches her first Pokemon, and then crushes the first Gym thanks to Zack accidentally using a Shadow move. When naming it my first thought was Shadow Punch, but uh, yeaaaahhhh. Next chapter Lily moves on through Johto. Little does she know, gyms won't always be this easy. Please favorite, follow, and review!