You might ask what happened to those Organizations(example Team Rocket), well most were disbanded, he crippled Giovanni before he busted the whole Team Rocket.
It also happened to the other organizations, Team Aqua and Magma disbanded after all their plans were idiotic, Team Galactic vanished from the world(he send them to the outer space were they died from the lack of oxygen, it may seems this is heartless but those guys causes mass destruction and even destroy the world, he does not follow the good and evil principles.)
Team Plasma disbanded after finding out that Ghetsis and Colress were murdered in their respective room, then the police unexpectedly barge in their hideouts.
Team Flare members were the same as Team Rocket, they disbanded after their leader was crippled and sent to prison.
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Pokemon League(Kalos) Finals
Alain vs Ash
"Let the match begin!"
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It was Alain last pokemon and Ash third pokemon(he only lost one pokemon.)
"Go! Charizard!"
"Greninja."
They both release their pokemon.
"Charizard! Mega evolve!!"
Alain's Charizard transformed into his mega state. Ash gaze at the transformation and grinned.
"Use flamethrower!"
Charizard breath a huge blue flame as it travels to Greninja, Ash didn't said anything and just smiled.
*BOOMMM!!*
Alain stared at the smoke expecting an injured pokemon only to see a burned crater. A flashing blue light appeared as the Charizard was hit by a water shuriken.
Greninja descended from above and landed on the ground.
"I haven't showed it to anyone but I think it's time to show something cool."
Ash said as he and Greninja glowed blue.
The people murmured in surprise, Sycamore stared at the show eyes wide.
"Greninja! Let's take this to another level!"
"Jahhhh!"
Ash glowed brightly and so Greninja. Suddenly Greninja was covered in swirling water and burst, there stood a Greninja with more features.
Mega Greninja
The people watching the battle gasps in surprise and started cheering for witnessing such phenomena.
From above were two champion sat, Diantha the Kalos champion stood up and stared wide eyes and her body trembling in excitement, while Steven of Hoenn jaw's dropped and eyes sparkling.
"How?...." Alain stared in surprise, never in life he saw a mega evolution without the use of the stones.
"What!!??" prof. Sycamore stood up mouth open and closing with his eyes wide in shock. "Such phenomena!!" he shivered in excitement.
"Don't be surprised, there are other pokemons that can mega evolve without the stones." Ash said with a smug face.
"What an unbelievable sight!! Ash Ketchum showed us an unbelievable mega evolution!! And he said other pokemons can mega evolve without mega stones is this true!!??"
"AAAAHHHHHH!!!!!!"
The croud cheered louder. The champions stared at Ash in surprise while Sycamore began shaking his assistant.
"Water severing waves!" Ash said, as ball of water forms in front of Greninja and high pressurized water burst from it.
Alain came out of his shock and commanded Charizard to dodge.
In the end Ash won the League.
Ash was in the waiting room getting back his bag as two champion and a professor entered.
"Ohh… it's just you guys." Ash said nonchalant and carried his bag.
The people entered the room gape at his nonchalant words.
"Ahem! Hello Ash we meet again, after that fantastic battle I would like to know about your Greninja." Sycamore said with a smile on his face. Ash stared at him and quickly walk to the exit, "Not available.".
"Wait!!" the three screamed and followed Ash as he halt and turned around.
"Fine! It was bond evolution the stronger the bond between you and your pokemon, there's a chance that you can do what I did." he said with an annoyed expression.
"So Steven how was your back?" Ash ask Steven with a knowing smile. He flinched and blushed hard.
Diantha stared at them and dismiss her growing thoughts(she thought they had sex.), "I would like to congratulate you on your battle." Ash stared at her, "Go on." Diantha sweatdrop "Ah–well– I would like to know if I can do it with my pokemons."
"I think you should stop it, the consequences of this evolution is big and might cost your life." he said with a serious expression. "How—" Sycamore was cut off.
"It connects your body with your pokemon, you can feel what your pokemon feels." Ash said.
"So you will feel the pain of your pokemon?" Sycamore muttered in shock.
"Your Pokemons have high pain tolerance while you don't. If your pokemons received big damage from an attack, your body might or will collapse." Ash stared at the silent trio.
"Thank you for the information Ash." Steven said and Ash smirk at him.
"What ever you do, don't the same as me I even fainted for the first time and woke up two days later." thats a lie, he use his aura for the evolution and not connecting the soul(using the evolution the two must connect their soul to form a bond that will boost the trainer and the pokemon will undergo an evolution.).
"See you next time." Ash walks out of the room.
"Hahhh I was really excited of this new discovery, well it is risky." Sycamore sighed and exits the room.
"Well that's it, I just want to know more maybe next time." Diantha soon followed.
"Wait for me!" Steven screamed.
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"Talonflame let's go." Ash said and mounted his pokemon. "Talonnnn!!" Talonflame flew at the speed of sound.
In mere minutes they arrived at the airport.
"Thanks bud and get some rest." Ash smiled at his pokemon and took his pokeball, the fire bird proudly raised its wings.
Ash stared at the windows recalling his previous adventure, after this he'll stay home and again, new adventure. He straightened up as a familiar presence entered his mind.
"Choosen one." a majestic voice entered his ear. "Arceus." Ash said, "Is there something you need?"
"I request your help, an old enemy has broken his prison and is on his way to destroy the Universe." Arceus voice carried seriousness.
Ash frowned who is this enemy? "Can I know who's the enemy?"
"Before the existence of Dialga and Palkia there was a pokemon far older than them, Nyxeus the night, he was the night and darkness, his power corrupted his core and started destroying the creation, and so I sealed him of and now he broke his prison and his goal is to steal the core of the choosen one." Arceus revealed. He froze in shock, "Me?"
"When I said that there are many universe, he right now is on the main universe and the choosen one is weakened." Arceus said, "He choose that moment and tried to steal his core, I request you to help the choosen one."
"I haven't told my mom that I'm going home so it's fine and she had Daisy, so I'm in!" Ash exclaimed in excitement. Arceus chuckled, "Be careful Ash he's strong, stronger than my eldest."
"I'll go alone, I'm leaving my pokemons" Ash said as Arceus asked in concern, "Are you fine without them?" Ash shook his head and smile, "I'm far stronger than any of my pokemon and with your gift I'd be safe."
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"Are you ready Ash?"
"I'm ready Arceus."
"Very well, I'll open the entrance to the main universe."
A blue spacial portal opened infront of him.
"This will be fun."
He walked inside the portal as it close.