(Location: Unknown island)

It was a nice sunny day with clear blue skies and clear blue ocean, waving through the ocean gently and calmly with no other pokemon in site. We then see an island that seems to be just filled with rocks and nothing else. No human life nor no pokemon life living on the island.

That is until something came down from the sky and landed at the edge of the island. A mysterious human like pokemon with a long tail landed onto the island with a mysterious and high tech helmet that he takes off and drops it onto the ground.

He then turns to the ocean to face the waters while we get a clear look at his face as he is like a alien like pokemon as he stares at the ocean what seems like minutes.

???: Who am I? Where am I? Who wanted me to be created? Who asked for me to be created? I despise everything connected with my creation!

Then suddenly a portal opens behind him which he turns to see the mysterious portal appear behind him and then Megatron step out through the portal alone as he walks up to him and stops at the two race stare at each other.

Megatron: So you must be Mewtwo. Made by the humans to serve as a weapon for mess destruction.

Mewtwo: Who are you?

Megatron: I am Lord Megatron, leader of the Decepticons and I have come to give you a offer.

Mewtwo: I am not interested being the humans slave and never will be.

Megatron: Ah you are mistaken. We do not work with humans, in fact we despise all humans and we wish to take control over them and I think you know how.

Mewtwo:.....Why me?

Megatron: Because you were used by humans as weapons for their goal of taking over the world. You wish to take revenge on the humans who have created you only to make you as a weapon. So what about we work together Mewtwo and together we will take over this planet and make the humans all pay for your creation.

Mewtwo stares at Megatron and starts to think aboit the offer and believes that all humans must pay for his creation. He then floats up into the air hovers over towards him as Mewtwo ask him.

Mewtwo: What can you give me once we work together?

Megatron: (smirk) Anything you want. We can make you a base, an army and so much more. As long we stick together and all that, we should be fine.

Mewtwo: Very well then. I will join your faction and together we will make all humans pay. This is the day that we will strike back!

(Several days later)
(Location: Ark Bridge)

At the bridge of the Ark we see Y/n and his team with Optimus prime, Wheeljack and Perceptor as Perceptor shows a news report about a storm happening at a city which Turbospike spoke up.

Turbospike: It seems like a heavy storm and so what?

Perceptor: Well it's very weird that a storm would suddenly came out of nowhere like that and it seems to be forced on one city which had a docks for boats.

Turbospike: Hhhhhhmmmmmmm yeah I kinda don't get it.

Y/n: Can it be just a normal storm?

Wheeljack: You could be right but we've detected a large amount of energon readings in the middle of the storm.

Then a image of the storm with a huge circle in the middle is shown as the rest look at it.

Alex: How did the drones managed to detected while being within a storm?

Wheeljack: Our drone can survive anything out there. We'll sometimes.

Perceptor: Plus we haven't gotten any reports about a Decepticons activity for a while. If the Decepticons are in the middle of that Island then which ment they are up to no good.

Verity: Did they make a weather machine?

Sorrel: That would be impossible but since they are from another planet with high technology, then it's possible.

Y/n: Optimus allow me and my team to head there and investigate it. We will find out what the Decepticons are up to.

Optimus prime: I believe that is impossible. We make have coordination of the storm but we don't know if there is a island that we can set the coordinations on to in our ground bridge.

Wheeljack: Besides it be risky since the storm will blow you all away within cycles.

Alex: Then what about find Punch's coordinations?

They turn to Alex which he look at everyone and continues on saying.

Alex: What? If we set the coordinations to where Punch is at, we can just open a ground Bridge and be there within seconds without any risky.

Wheeljack: Have you not forgotten that Punch is literally I a Decepticon flag ship? That's all too risky.

Optimus prime: But....it might work. Perceptor, connected Punch and have him find a safe area for Y/n and his team.

Perceptor: Right away sir.

Optimus prime: Y/n, you and your team will head to the Decepticons flag ship and find out what they are planning. We shall not allow them to complete their goal.

Y/n: (salute) You can count on us sir.

And so Y/n and his team head off for their mission while Optimus Prime turns to the monitor and look around the storm and wonders what it could be.

Mew.

Then Optimus prime turns around and looks around onky to see nothing but he felt something and he felt like he must find it. So when Ironhide enter the bridge Optimus prime walks up to him and tells him.

Optimus prime: Ironhide your incharge once I'm back.

Ironhide: On it prime.

And so Optimus prime make his leave to find whatever he is looking for and maybe this might answer his question about what possible threat the Decepticons might have.

(Location: Nemesis storage room)

We see Counterpunch looking around for any Decepticons and waiting for Y/n and his team. Seconds later a ground bridge open and Y/n and his team walk out from the grounr Bridge as CounterPunch transforms into Punch and walks up to them while the ground bridge closes behind them.

Punch: It was a risk to be using a ground Bridge to get here but your lucky there is only some Decepticons here at the Nemesis.

Y/n: (smile) Well glad to see you Punch. Meet any nee friends?

Punch: (chuckle) You wouldn't believe me if I said I did. (Noticed Y/n, Ben, Verity and Sorrel) I see you brought the humans here? Isn't it dangerous?

Alex: (smile) We been through dangerous situations. Hasn't stop us.

Punch: Guess so. Follow me and stay close.

They agree and they follow Punch as they exit out of the storage room and make their way through the hallway as they check around for any Decepticons that might come around the corner.

They only see a few Decepticons but they were just walking around and doing nothing so they continue sneaking around as Madison ask Punhc.

Madison: So what are the Decepticons doing?

Punch: Can't say doe sure. We were in the sky but then we parked underwater with a island on top of us.

Turbospike: A island on top of us?

Y/n: Did they made a base on a island?

Punch: Seems like it. Turns out Megatron made an allie and now they have a huge bass up there and it's unknown what they are doing right now.

Turbospike: I thought you were spying on them?

Punch: Just because I'm a great Decepticon that doesn't mean I'm not allow to know information about what Megatron and the rest are up to. Whatever is going on up there, they are up to no good.

Alex: Hey I see a elevator up ahead.

They see it as well as they walk towards it but Punch stops them and hides them as the elevator doors open and two Decepticon seekers step out and walk off whioe the Autobots hide for a while.

Then once they are gone they step out and Y/n and his team enter he elevator while Punch stands outside od the elevator.

Y/n: What about you?

Punch: Sorry but someone has to delete the security footage before any Decepticons know you guys are here. (Transforms into CounterPunch) Good luck you guys.

He then walk off as the elevator doors close and they go up and see what the Decepticons are up to and they hope they can stop them.

(Meanwhile)

We see a cave within a island along with a small wooden dock for boats to arrive as we see a mysterious women covered with clothes apart of her face standing and waiting when a repotic hand came out from the water and grab at the shore and soon he came out of the water.

The women watches as the Autobot named Hot Rod comes out of the water while holding Ash and Pikachu along with Bumblebee with Misty and Togepi, Jazz with Brock and Sideswipe comes out of the water as they climb out of the water.

They set Ash, Pikachu, Misty, Togepi and Brock down as Hot Rod gets up and says in a cheerful tone.

Hot Rod: (smile) Looks like we made it.

Jazz: Seems like it. Next time, no more boat rides, especially with Team Rocket is on board.

Sideswipe: How did they get a boat?

Jazz: No idea.

Bumblebee: You guys okay?

Misty: Yeah we're fine. Thank you Bumblebee.

???: You have arrived just in time. Please follow me.

And so they did as they follow her up the steps while Brock stares at the women for a bit.

Sideswipe: What is it Brock?

Brock: I feel like I've seen her before.

Sideswipe: Yeah probably best leave your love story after we meet this greatest pokemon trainer ever.

Bumblebee: (smile) I'm very excited to see who he is. I've never know you humans have the greatest pokemon trainer?

Ash: (smirk) Us to but I'll beat him and proof myself to be the best pokemon trainer ever.

Pikachu: (smile) Pika!

Hot Rod: (smile) Heck yeah!

Jazz: Still I find this a bit spooky. Anyone got those bad feelings about this?

Soon they reach to the top and soon they make theie walk down the hallway and soon arrived to two large doors which the doors open. Once the doors fully open they see what seems like a large room with a table with food on it as they step inside and see three pokemon trainers already here and have their pokemons out to run away for a bit.

Hot Rod: (smile) Seriously? Where's the music and Where's everyone else? If we want have a party then let's get thid party started.

???: (smile) Huh those four are some weird pokemon.

Sideswipe: Hate to burst your bubbles but we're not pokemon.

Corey: (surprised) That's surprising. Anyways the names Corey.

Fergus: (smile) I'm Fergus.

Neesaha: (smile) And I'm Neesaha.

Then Brock place his hand on the table while standing in front of Neesaha while he tells her.

Brock: (smile) Just lovely. Blastoise, Dewgong, Vilpume, Ninetales, Rapidash and your Wigglytuff, too! And yet, nothing can compare to their lovely trainer! Your boundless beauty. My queen. My lady, once this storm passes, let's gaze upon the sun-drenched seas and eat my famous jelly donut made with love-

Then Misty pulls his ear and drag him away while saying.

Misty: Yeah, Yeah, if you're going to eat, you're better off eating alone.

Ash and the others giggle a bit when suddenly the lights came off accept for the circle staircase where the mysterious women stands next to as she turns to everyone and tells them all.

???: My master is now ready. Right now you are seeing the greatest pokemon trainer alive.

Then they all look up and sees something floating down which surprised everyone as the figure floats down and soon lands onto the ground while the mysterious women gose on to say.

???: Not only he is the greatest pokemon trainer but he is also the greatest pokemon ever. Allow me to introduce to you all my master, Mewtwo.

Then the lights came back on as they see Mewtwo which surprised and confused everyone.

Jazz: That's one mysterious pokemon.

Hot Rod: Yeah but one cool Pokemon.

Fergus: Hang on a minute! A pokemon can't be a pokemon trainer!

Mewtwo/???: Are you sure about that?

Bumblebee: Um did I hear that correctly? Did they spoke at the same time?

Brock: That's telepathy.

Hot Rod: Why do I get a feeling that's going to be overused?

Mewtwo/???: I am the one who choose my own rules.

Fergus: If this is a bad joke, I'm going home!

???: I'm afraid you won't be leaving humans.

Suddenly Starscream and other Decepticon came out of nowhere as they surrounded them while aiming their blasters at them which shocked everyone.

Corey: More gaint robots!

Sideswipe: Yeah but they are worse.

Then Megatron appear as he stand beside Mewtwo as he stare at everyone in the room while he smiled at them.

Megatron: (smile) Hello there humans and Autobots. Welcome to the party, a party that we will take over this planet for the Decepticon cost.

Hot Rod: I don't think so Megatron!

He fired a shot at Megatron but suddenly I froze inches from Megatron. Everyone was shcoked to see Mewtwo is stopping the shot and he returns it back at Hot Rod which gets hit and was sent flying and crash onto the wall and land hard onto the ground.

Jazz: Hot Rod!

The Autobots rushed over to him and help him up. The other Decepticons aim their guns at them as they surrounded them while Megatron tuene to Mewtwo and ask him.

Megatron: (smirk) I believe now it's time to ditch our doll.

Mewtwo: Agree. (Turns to ???) You are free now.

Suddenly the women Snape out of her control and stumble forward a bit and fell but Brock catched her and her hat fell and revealed to be Nurse Joy.

Brock: (surprised) Nurse Joy?

She open her eyes and sat up and looks around and ask.

Nurse Joy: Where I'm I? The last time I remember I was walking him when a huge robot kidnapped me.

Megatron: We have you under Mewtwo's control to not only to see his test of strength but to have you to lower any of the most strongest pokemon trainers to this island.

Brock: What do you mean?!

Megatron: (smirk) You see Mewtwo has join sides with the Decepticons to have one goal and that is to take over this planet and rule all humans. In order to do that we needed a pokemon army that is strong enough to take on anything that stood against its way. Now we have gather you all here and now our plan of making a Clone army of pokemon will begin.

Ash: Clone pokemons?

Hot Rod, Bumblebee, Sideswipe and Jazz were stripped from their weapons and on their knees as Hot Rod looks up at Megatron and tells him.

Hot Rod: Your plan will never be completed. The Autobots will stop you for sure.

Megatron: (evil laughter) The Autobots will not know what will hit them! Optimus and his Autobots will be crush by our hands and no one will not warn them. Not even you all. (Turns to Starscream) Starscream, take them to the prison cell and kept them there.

Starscream: (smirk) As you wish Lord Megatron.

He takes Hot Rod and his team away and now it was just Ash and the other humans and pokemon as Megatron looks at them and tells them.

Megatron: (smirk) Now that's done with, it's time for our first test. (Call in Shockwave) Shockwave, are the clones resay for combat?

Shockwave: (coms) Yes Lord Megatron.

Megatron: (smirk) Then you know what to do.

Then we cut to Shockwave within a huge lab somewhere at he base along with a machine next to him as he push some buttons and then looks over and see three test tubs that start to bubble up and then the test tubs open to reveal cloned versions of Charizard, Blastoise and Venusaur. Soon the Cloned Charizard's eyes open and they arecready for their first combat test.

To be continued.............................