Author's Note: This was the most voted one , so it comes first , this is a flashback long due of the events of SS anne , or exactly what happened from the Champions perspective .
Lance's POV
The phone call with the Ace Operatives stationed in Celadon City had gone on for far longer than I had expected.
A few days ago, the therapist assigned to the winners of the S.S. Anne Tournament had quietly submitted a report to the League. One of the trainers had expressed concerns about possible criminal activity surrounding the Game Corner in Celadon City. On its own, it wasn't enough evidence for the League to raid a licensed business. Acting purely on a suspicion would set a dangerous precedent.
Still, we hadn't ignored it either.
The local police had been instructed to quietly increase surveillance around the area, and several League agents had been deployed undercover to gather more information.
Now that decision had paid off.
The report I was currently reading confirmed what we had feared.
Team Rocket.
The Game Corner had indeed been one of their major operational bases.
"..."
I rubbed the bridge of my nose.
Apparently that Red kid had somehow gotten himself tangled in the middle of the entire mess as well. Thankfully, the undercover operatives reacted quickly enough to support the police, preventing what could have become an even bigger disaster.
Unfortunately...
Celadon City wasn't coming out of this unharmed.
Cornered with no viable escape route, Team Rocket had detonated large sections of their underground base in an attempt to destroy evidence and cover their retreat. The resulting explosions had damaged nearby buildings and started several fires before the emergency services finally managed to contain them.
"...Damn it."
Every single time Team Rocket appeared, they somehow managed to leave an entire city cleaning up after them.
Just hearing their name was enough to irritate me nowadays.
Especially after everything that had happened aboard the S.S. Anne.
Thinking back to that incident alone was enough to give me a headache.
For nearly two straight days I'd done nothing except write reports, attend emergency meetings, brief League executives, answer questions from the International Police, and explain the situation over and over again to the other members of the Elite Four of that incident.
My fingers unconsciously tightened around the report lying on my desk.
There was still one problem that remained unresolved.
One Pokémon.
One existence.
A creature so overwhelmingly powerful that even thinking about it left a bitter taste in my mouth.
Mewtwo.
The League's search had continued ever since the incident aboard the S.S. Anne.
Personally.
I had made sure of it.
Every available lead had been investigated. Rangers, League scouts, trusted Ace Trainers even a few specialists capable of tracking Psychic-type Pokémon had been quietly brought into the search.
Nothing.
It was as if the Pokémon had simply vanished from Kanto.
Which, knowing what I had witnessed...
Was entirely possible.
I still remembered those violet eyes.
The calm way it had looked at every Champion, Elite Four member, and Rocket Executive present.
Not with arrogance.
Not with hatred.
Simply...
With disappointment.
And despite possessing strength that surpassed almost every Pokémon I had ever encountered...
It had spoken only a few words that still lingered in my mind.
"I am... still too weak."
I slowly leaned back in my chair, letting out a long sigh.
"...What kind of monster believes it's weak after showing power like that?"
My office fell silent.
Outside, Indigo Plateau continued functioning as though it were any other day.
League officials hurried through the hallways carrying documents.
Secretaries organized the next series of meetings.
Somewhere below, trainers continued challenging the Indigo Conference facilities, completely unaware of the discussions happening at the highest level of the League.
I closed my eyes.
No...
There was no point dwelling on it now.
Because every time I thought about the S.S. Anne...
My mind always drifted back to that day.
To the cruise ship.
To Team Rocket's attack.
And to the impossible events that followed.
———————————————————-
Flashback
Third POV
After cutting through the remaining Rocket grunts and defeating several of the stronger members with relative ease, the Champions were finally making their way toward the lower decks where the rookie trainers were being attacked .
Then...
Reality itself seemed to bend.
Before any of them could react, an overwhelming wave of psychic energy swallowed the four Champions whole. None of them even had time to call out a command before the scenery around them twisted.
The next instant, Lance, Steven, Diantha and Alder found themselves standing atop the highest deck of the S.S. Anne.
The cold ocean wind whipped across the burning cruise ship while smoke rose from several damaged sections below. The sounds of explosions and distant battles still echoed through the night, but atop the deck there was only silence.
Waiting for them was a lone Pokémon.
Its entire body was concealed beneath an unfamiliar metallic armour that looked more like restraints than protection. Purple eyes calmly studied each of the four Champions without the slightest hint of fear.
The strange Pokémon floated a few feet above the deck before finally speaking.
"So..."
"You are the so-called Champions he warned me about."
"You were to be eliminated quickly..."
"...or stalled."
Lance narrowed his eyes.
"What... are you?"
He had read records of legendary Pokémon.
Yet never had he seen anything even remotely resembling this creature.
The unknown Pokémon looked directly at him.
"I am Mewtwo."
"The strongest Pokémon ever created."
For a brief second...
None of the Champions spoke.
Then Steven quietly adjusted his tie.
"Whatever you are..."
"You picked the wrong people to stand in front of."
There was no need for further discussion.
Four Poké Balls shot into the air almost simultaneously.
"Metagross!"
"Gardevoir!"
"Volcarona!"
"Charizard!"
The four ace Pokémon landed around Mewtwo, surrounding him from every direction.
The battle erupted immediately.
Charizard opened with a massive Flamethrower that swept across half the deck.
Volcarona followed behind it, releasing Fiery Dance to box Mewtwo into one side.
Metagross came crashing down from above with Meteor Mash while Gardevoir launched a perfectly timed Shadow Ball to cut off any escape route.
For a normal Pokémon...
The battle would already have been over.
Mewtwo simply disappeared.
Teleport.
The flames collided with one another instead.
He instantly reappeared behind Charizard and fired an unfamiliar psychic attack.
"Psyshock!"
The condensed psychic force slammed into Charizard, forcing him backwards despite resisting Psychic attacks better than most Pokémon.
Mewtwo Teleported again.
Another Shadow Ball narrowly missed him.
Then another.
And another.
The entire deck became a blur of movement as attacks continuously crossed one another.
Meteor Mash collided with Psychic.
Shadow Ball met Shadow Ball.
Dragon Claw scraped against Reflect before sparks exploded across the battlefield.
Even Lance couldn't help but notice how composed Mewtwo remained throughout the exchange.
The creature wasn't panicking.
It was calmly analysing each of their Pokémon.
Steven noticed it as well.
"It's learning."
Alder clicked his tongue.
"Then don't let it."
"Volcarona!"
"Bug Buzz!"
The moth Pokémon's wings vibrated violently.
A concentrated wave of high-frequency sound burst across the battlefield.
Unlike the previous attacks...
This one landed cleanly.
The buzzing seemed to directly interfere with Mewtwo's psychic concentration.
For the first time...
The mysterious Pokémon actually reacted.
His hands instinctively rose to the sides of his helmet as Bug Buzz continued tearing through him.
The opening lasted barely a second.
It was enough.
"Now!"
Metagross descended like a meteor.
"Meteor Mash!"
At the exact same moment Charizard charged from the opposite side.
"Dragon Claw!"
The steel fist and draconic claws landed together.
BOOM!!
The force of the combined attack launched Mewtwo across the deck.
Steel railings shattered.
Several ventilation units were completely destroyed before Mewtwo finally crashed into one of the ship's communication towers.
Silence.
Then...
Crack.
A fracture spread across the strange armour covering his body.
Another followed.
Then another.
Charizard's Dragon Claw had sliced deep through one side of the armour while Metagross' Meteor Mash had completely caved in the front.
Large metallic pieces began falling onto the deck one after another.
For a brief moment...
The Champions thought they had finally gained momentum.
Then Steven's expression suddenly changed.
"...Something's wrong."
His Metagross instinctively stepped backwards.
Across the battlefield, Diantha noticed Gardevoir trembling.
Not from fear...
From instinct.
As one of the strongest Psychic Pokémon alive, Gardevoir could feel exactly what was happening.
The armour...
Hadn't been protecting Mewtwo.
It had been suppressing him.
The remaining fragments slowly floated into the air.
Mewtwo calmly looked at the broken restraints covering his body.
"I no longer require these."
With a flick of psychic energy...
Every remaining piece shattered into dust.
Then a soft emerald glow enveloped his body.
Recover.
Every bruise disappeared.
Every cut closed.
His breathing returned to normal.
The next second...
The psychic pressure exploded outward.
The deck itself groaned.
Loose debris began floating into the air.
Even the ocean around the ship rippled unnaturally under the sheer weight of Mewtwo's psychic aura.
Steven and Diantha immediately realized the same terrifying truth.
This wasn't simply powerful.
This was one of the strongest concentrations of psychic energy either of them had ever sensed.
Mewtwo vanished again.
This time...
Even Gardevoir struggled to follow.
He appeared behind Charizard, firing a Shadow Ball before instantly teleporting above Metagross to launch Psyshock.
Before either attack even finished, he had already moved again, striking Volcarona with Psychic and forcing Alder's ace backwards.
The battle had completely changed.
Lance's Charizard was forced onto the defensive.
Metagross was no longer dictating the pace.
Even Gardevoir was beginning to lose track of Mewtwo's movements.
Lance slowly reached toward the Key Stone hanging around his neck.
"...He was holding back."
Steven nodded while unclipping his own.
"So much for ending this quickly."
Diantha smiled faintly.
"I suppose..."
"...we stop holding back too."
Three Key Stones suddenly began shining brilliantly.
Rainbow-colored energy linked trainer and partner.
The bonds they had forged over countless battles resonated.
"Mega Evolve!"
Blinding white light engulfed the battlefield.
Charizard's orange scales darkened into jet black as brilliant blue flames erupted from his mouth and tail. His body grew more muscular, powerful draconic wings spread wide, and an overwhelming dragon aura radiated from every movement.
It became Mega Charizard X.
Metagross' already imposing body transformed into something even more terrifying. Four additional metallic limbs unfolded around him as his body streamlined into a sleeker yet far deadlier form. Psychic energy continuously pulsed through every joint while his hovering speed nearly doubled.
It became Mega Metagross.
Gardevoir gracefully floated higher into the air as her elegant white gown expanded into a magnificent flowing dress. Emerald hair cascaded far longer than before, while shimmering psychic energy surrounded her like countless ribbons dancing through the wind, giving her the appearance of a queen descending onto the battlefield.
It became Mega Gardevoir.
For the first time since the battle had begun...
Mewtwo stopped.
His violet eyes quietly observed the three transformed Pokémon standing before him.
"...Interesting."
———————————
The battle from then onward became even faster and far more dangerous.
Every second, another powerful attack lit up the night sky above the S.S. Anne.
Gardevoir continuously supported the team from the rear, using Heal Pulse whenever one of the Champion's Pokémon was pushed back. Whenever Charizard or Metagross took a heavy hit, a gentle wave of healing energy would wash over them before they charged back into battle.
Mewtwo, meanwhile, relied entirely on Recover.
It was the only reason the battle remained even remotely competitive.
Without it, the combined assault of four Champion aces would have overwhelmed him long ago.
A blue Flamethrower from Mega Charizard X forced Mewtwo to erect Reflect.
The barrier barely lasted a moment before Mega Metagross shattered it with a devastating Meteor Mash.
The impact launched Mewtwo backwards, only for Mega Gardevoir to Teleport directly beside him and slam a Shadow Ball into his side.
Before he could even recover, Volcarona, now having stacked several Quiver Dances, released an amplified Bug Buzz.
The high-frequency wave crashed into Mewtwo once again.
"...!"
He instinctively covered his ears as the attack tore through his concentration.
The Champions pressed the advantage immediately.
Dragon Claw.
Meteor Mash.
Shadow Ball.
Bug Buzz.
Attack after attack landed one after another, forcing Mewtwo to repeatedly use Recover just to remain standing.
The Champions had finally begun pushing him back.
Then...
Mewtwo suddenly stopped attacking.
He floated silently in the air.
His Recover finished healing the last of his injuries.
Then...
He laughed.
Not an angry laugh.
Not a mocking one.
A laugh filled with realization.
"...Hahaha..."
"So..."
"He lied to me."
The Champions hesitated.
Mewtwo slowly looked at his own hands.
"Learning control..."
"Wearing those restraints..."
"It was all a lie."
"I understand now."
"He never wanted me to learn control."
"He wanted to control me..."
"...by keeping me weak."
His gaze slowly shifted toward the three Mega Evolved Pokémon before him.
"Mega Evolution..."
"So this is a power born from trust."
The psychic Pokémon's eyes gleamed with curiosity rather than jealousy.
"This..."
"...is what I wish to pursue."
Lance stepped forward atop Charizard.
"Mega Evolution isn't something you can simply obtain."
"It is born from the bond between trainer and Pokémon."
"It is their trust in one another that allows aura to resonate and grant power beyond normal evolution."
Mewtwo remained silent for a few moments.
Then he smiled faintly.
"So..."
"You are saying Pokémon require humans to become stronger."
"That is your answer."
Lance shook his head.
"No."
"I'm saying the right partner can help you reach heights you couldn't alone."
Mewtwo considered those words.
"...Perhaps."
"But I shall be the judge of that."
"I now know one thing."
"I will never grow stronger by remaining beside him."
"He only wished to use me."
Lance's expression hardened.
"Him?"
"Who created you?"
"Who was using you?"
Mewtwo answered without emotion.
"The leader of Team Rocket."
Silence fell across the battlefield.
Even Steven's usually composed expression cracked slightly.
The leader...
Then Mewtwo chuckled again.
"I suppose..."
"I should thank you."
The Champions looked at him cautiously.
"You broke my restraints."
"You showed me a path to greater strength."
"And most importantly..."
"...you opened my eyes."
"I will no longer serve that lying rat."
Instead of taking another battle stance, Mewtwo slowly began floating higher into the night sky.
"I shall travel this world."
"I shall learn who I truly am."
"I shall discover strength beyond anything he imagined."
His eyes lingered on the three Mega Evolved Pokémon.
"And one day..."
"...I will surpass your Mega Evolution."
Psychic energy engulfed his body.
Lance immediately shouted,
"Stop him!"
Charizard, Metagross and Gardevoir all lunged forward.
Too late.
Teleport.
Mewtwo vanished without leaving behind even a trace of psychic residue.
Only silence remained atop the battered S.S. Anne.
Lance let out a long sigh as the memory faded.
The aftermath of Mewtwo's disappearance had been almost as chaotic as the battle itself.
Across the ship, Team Rocket operatives panicked after realizing their greatest weapon had abandoned them. Many immediately attempted to flee using Psychic-types capable of Teleport.
Some escaped.
Many didn't.
Ace Trainers had already surrounded the ship with Pokémon possessing abilities and moves such as Shadow Tag, Mean Look, and Arena Trap specifically to prevent Rocket members from fleeing.
By dawn, most of the remaining operatives had been arrested.
Yet none of it mattered.
The one being they truly wanted to find...
Had disappeared.
Lance had personally ordered the League to dedicate significant resources toward locating Mewtwo, but months had passed without a single credible sighting.
Fortunately, the Champions of the other regions had openly offered Kanto their support after the S.S. Anne incident.
It was one less burden on his shoulders.
Still...
Lance stared out the window of his office.
He wasn't worried about the Mewtwo he had fought that day.
He was worried about the Mewtwo that would continue growing stronger.
And somehow...
He had a feeling that the next time they met if they ever meet...
That battle would be far more difficult than the last.
Author's Note: I always had the dilemma of how to show mewtwo but this is my best attempt at it , I did think of taking traveller fic as reference but the legendaries there are too strong , here also they would be strong just not unbeatable at least like mewtwo , arceus or the creation trio are a different story of course. Mewtwo here is strong , but it wasnt at its best, throughout its life until now it was restricted with the armor as giovanni wanted some control over it ,so even it never tried its full power before this incident and it was fighting 3 mega and a volcarona arguably a very dangerous counter to it .
One big change unlike cannon mewtwo escapes team rocket way earlier and thats gonna have massive ramifications , infact mewtwo's outlook of life itself has changed unlike in cannon of the movie where it hated humans , here it has seen mega evolution so its outlook has changed and it hasnt seen enough evil as its stay with team rocket has been less .
Also Lance might try for the champion spot for Kanto soon after the indigo league I guess. As he has a check for lorelei now.
I also already dropped hint of what interlude celadon city is.