AN: I was no a bit of a roll and I wanted to get this this, even though I cut out one thing that will be put in a later chapter.
Chapter 3: Surprises
During the three days they group was on the ship, Latias started teaching her brother how to use telepathy with minor results. Latios was able to use telepathy, but a few simple words a minute. Ash battled two trainers on the boat, one being a rookie trainer with a Rattata and the other being a top thirty-two in the Johto League. Ash used Pikachu on the newer trainer and won in a one on one match. But in the match against the second trainer it was a four on four. Ash had Pikachu go first, who knocked out the first two, almost three, before being taken out by a Hitmontop. Latias went in before Ash could decide which of his new Pokemon to pick next. Latias knocked out the remaining two Pokemon winning the battle.
As the ship was docked at Goldenrod City's harbor, Ash and his Pokemon went on a search for the Gym. After an hour and half, not including lunch, the group found the gym. They went behind the gym, but no one was there, not even a Rattata.
"Mewtwo." Ash called, but received no response. "Mewtwo." No response.
'Ash, I don't think he is here. Let's come back here later.' the female Eon said.
"Maybe you're right." Ash said before the back door of the gym opened. The three legendaries turned invisible while Ash turned and saw the gym leader of the gym, Whitney.
"Why are you back here and who were you talking, too?" the pink-haired gym leader asked.
"I was hoping to meet an old friend and I was agreeing with…" Ash said before he noticed the three legendary were invisible. "Meloetta, Latias, Latios, it's okay. This is Whitney, the gym leader here." Whitney thought Ash was crazy before Latias appeared next to Ash.
"Wow, a Latias." Whitney said before the other two legendaries dispelled their illusion. A Latios and Meloetta, too."
"Hey, Whitney." the raven-haired trainer said.
"Ash?" she said. "It's been a while hasn't it?"
"Yeah, it has." Ash said.
"So, who's your old friend?" Whitney asked.
"A Pokemon I meet after I got my badge from you." the Kanto naïve said.
"Does the Pokemon have a name?" the gym leader asked.
"I promised him, I won't tell anyone who he is." Ash said.
"Maybe it's the Pokemon the some people say that only roams around the city at night, but no one knows its name." Whitney guessed.
"Looks like we'll come back tonight." Ash said to the Pokemon.
"Wanna come in?" Whitney asked.
"Sure." Ash said.
As Whitney, Ash and his Pokemon enter the gym though the back, a male trainer was waiting on the battlefield.
"Whitney, I challenge you to a gym battle." he said.
"I'll be down in a minute to battle you." the gym leader said.
"Good luck, Whitney." Ash said as Whitney hurried down to the battlefield. Ash took a seat in the stands with Pikachu and Meloetta in his lap and the Eons next to him.
"Ready?" Whitney asked.
"Ready when you are." the trainer said.
"This is an official three on three match between the challenger Simon Williams from Violet City and the gym leader Whitney for the Plain Badge. Let the match begin." the referee said.
"I chose Nidorina." Whitney said as she let out her Nidorina.
"Come on out Butterfree." Simon said.
"Tackle attack Nidorina." Whitney told her Pokemon before she charged at the bug type.
"Counter it with gust." Simon ordered and the Butterfly Pokemon complied by sending a strong gust of wind that sent the poison-type few feet into the air and fifteen feet back.
"Nidorina." Whitney cried. Nidarina got up and charged in again.
"Psybeam." the challenger ordered. A multicolored beam hit the Poison Pin Pokemon and sent it to unconsciousness.
"Nidorina is unable to battle. The round goes to the challenger." the referee announced. "Whitney send out your next Pokemon."
"Your turn Clefairy." the pink haired leader said. "Clefairy use metronome." Clefairy started moving its arms left and right.
"Use psybeam before it finishes." the challenger said. A psybeam hit Clefairy and Clefairy didn't want to battle anymore.
"Clefairy has forfeited the match. This round goes to the challenger. Whitney send out your last Pokemon." the referee said.
"Milktank, come on out." Whitney called out. "Milktank, use rollout." Milktank
"Stop it with sleep powder." the challenger said. Butterfree covered he field with the sleeping powder, but it didn't affect Milktank's impact on the flying/bug- type.
"Butterfree." the trainer cried before it struggled up, ready to continue, but was stuck again by Milktank's rollout for the ending blow.
"Butterfree is unable to battle, the round goes to Whitney." the ref announced.
"I choose you, Noctowl." Simon said as a Noctowl swooped around the field.
"Milktank, keep it up." Whitney told the Milk Cow Pokémon, who was gaining more momentum by each passing second.
"Noctowl, use hypnosis." the Owl Pokemon's trainer ordered. Even though the attack hit its target, it was had no effect. "What?" the trainer said.
"Milktank's rollout makes it that Milktank can't make eye contact with your Noctowl." Whitney explained as her Pokemon made Noctowl get thrown in a wall, knocking it unconscious.
"Noctowl is unable to battle. Challenger call your next Pokemon." the ref said.
"Come on out, Bellsprout." the challenger called out. "Use ingrain." The Flower Pokemon put its roots into the ground before it got ran over by Milktank. "Vine whip." The vines got repelled off Milktank each time Bellsprout tried to it hit before Milktank ran over the grass/poison, again. "Keep trying." Simon said, but, to no avail, Bellsprout was knocked out in one final blow.
"Bellsprout is unable to battle. The winner of this round and match is Whitney." the ref announced.
'Why wouldn't any of the attack work on Milktank?' Latias asked to her trainer.
Overhearing their conversation, Whitney answered, "That's simple. When Milktank is using rollout, Milktank tucks in its head into its chest, making it that moves like sleep powder and hypnosis won't work, and the speed of Milktank's rollout counters most attacks."
While Whitney was answering Latias's question, the trainer that lost the match noticed Ash and his Pokemon and completely ignored the answer. When Whitney finished, he asked her, "When did you get legendaries?"
"Exactly, I caught them." Ash said.
"You're the one that beat Tobias's Latios and Darkria in semifinals of the Lily of the Valley Conference last year." Simon said.
'You two never told us that you battled another Latios.' the female Eon said.
Ash, surprised he got recognized by that battle, answered Latias first, "I didn't think you would be interested."
"How did get a Latias and Latios?" Violet City native asked.
"Latias and Latios wanted to come with me." Ash stated.
After Simon pelted Ash with questions for over ten minutes, Whitney, Ash, and his Pokemon were left alone. During that period time, they caught up.
As it started to get dark, Ash left the gym with two invisible, one disguised, and one mouse Pokemon. They headed to the Pokemon Center before Latias reminded Ash, 'Shouldn't we see if Mewtwo is behind the gym?'
"I completely forgot about that. Thanks, Latias." the trainer said before they turned around.
After a while, Ash admitted, "We're lost."
'This way.' Ash heard from a male voice in his head.
"Who said that?" Ash asked as the blue Eon showed himself. "That was you, Latios?" Latios nodded before he led the group back to the gym.
As they got behind the gym, they noticed a figure with a ragged, brown cloak over it.
'Hello, Ash,' the figure said via telepathy 'Meloetta, Latias, Latios.'
Recognizing the voice, Ash greeted back, "Good to see you, again, Mewtwo."
Mewtwo took off his hood as he said to Latios, 'I believe you have told him my conditions.'
"He has, but where are the others?" the Kanto trainer asked.
'You'll see, soon.' the Genetic Pokemon answered before teleporting the six of them to the last place Ash remembered meeting the clones.
'Where are we?' Latias asked.
'Inside Mount Quena.' Mewtwo said. 'Follow me.'
Mewtwo lead them to a spring inside the mountain that had the cloned Pokemon and some of their offspring. 'You all live here?' Latias asked.
'No. Most of us were not accepted by the species we were cloned from. After Arceus told me about his idea that you agreed to, they have agreed on allowing you, Ash, to capture them.' Mewtwo stated with nods around the spring agreeing to the statement.
"How do you think Professor Oak will react after this?" Ash asked his starter.
"Pi pikachu." he said with a shrug before yawning.
'Get some rest.' Mewtwo said, 'We'll talk in the morning.'
The next morning, Pikachu zapped Ash, the last one asleep, awake.
'Was that really necessary?' the red dragoness asked.
"Pi, pikachu." Pikachu said.
"Don't worry, Latias. I'm used to it." the trainer said before he noticed Suicune, Riakou, and Entei were in the cave. "Suicune, Riakou, Entei. When you come in?"
'Last night, Latios told Mewtwo that they were going to meet you on top of the mountain and Mewtwo and Latios brought them here while you were asleep.' Latias explained before they heard footsteps in the cave.
Meloetta, Latias, and Latios turned in visible before the one that ordered Mewtwo's creation to happen came into view.
'You.' Mewtwo said.
"It's been quite a while, Mewtwo." Giovanni said. "It seems you got me some welcoming gifts."
'How did you remember my existence? I wiped your memory of me.' Mewtwo said.
"But, you forgot to wipe my computers' memory." Giovanni stated.
'Leave.' the Genetic Pokemon told the crime boss.
"After what is mine is returned to me." the leader of Team Rocket stated, flatly.
'I don't belong to you or anyone else.' Mewtwo told.
"You will summit to my will. Perhaps, after you are under my control, I have you do what Hunter J failed to do."
Latias was angry at the fact the suited man in front of them was the one that hired Hunter J to kidnap her and Meloetta, who was too frighten to keep her invisibility going.
"I wonder want other surprises you have store for me, Mewtwo." Giovanni said as Ash put Meloetta in his own arms.
"I won't allow you to take any of them." Ash told the crime boss before reaching into his bag.
"Don't make me laugh." Giovanni said and he, unknowingly, made Latias pissed.
Latias dive bombed the Team Rocket leader as she said, 'Ash caught them while Latios and I keep them detracted.'
Ash pulled out multiple shrunken Pokeballs out his bag. "Mewtwo, I'll catch you first, so you can help them." Ash said before tossing a Pokeball at Mewtwo. The ball hit and absorbed the psychic-type. The ball didn't the wobble and Pikachu let the Genetic Pokemon out, who joined the the other two psychic-types, the legendary beasts, and Pikachu as many Team Rocket grunts approached the cave. Ash continued throwing Pokeball at the clones and, when all Pokeballs thrown at the Mewtwo's clones dinged, all, but one, teleported to Professor Oak's lab.
'Ash, we can't keep them back.' Latias said.
Ash picked up the Pokeball one the ground before he said, "Mewtwo, can teleport us out of here?"
'If everyone is near each other, I can get us far away from here.' Mewtwo said.
Ash ran to the Pokemon before he said, "Mewtwo, now."
On that note, Mewtwo teleported the eight of them away from the mountain.
Giovanni stomped his foot before he ordered the grunts, "Find them."
Ash and the group of Pokemon that was teleported, ended up teleporting in the middle of a Pokemon Center and startled the Nurse Joy in it. "What's…" she started to say before she noticed the three legendary beasts. "Suicune, Riakou, and Entei."
"Nurse Joy, where are we?" Ash asked as he was still comforting Meloetta.
"Ecruteak City's Pokemon Center."
AN: If anyone want to give me some ideas to get the story following more smoothly and be able to help get it updated more frequently, I would appreciate it very much.
Make sure to leave a review and suggestions.