At the cloning machine room we see sith Imperial troopers taking the DNA's of pokemon and placing them within the machine for cloning machine for cloning. While that's going on we see Team Rocket peaking out behind the boxes and watching them doing their work.

James: I don't like this one bit.

Jessie: Be quiet and come on.

They sneak around and trying to make their leave towards the door. They look over to the Sith Troopers, making sure they haven't spotted them as the pokemon clones were complete and was sent up to the surface while they get to the door and was just about to open it when they were caught.

Sigh Imperial trooper: Hey!

They froze and turn to face an Sith Imperial trooper walk over to them and stare at them for a moment and then ask.

Sith Imperial trooper: Who are you three?

Jessie: Uuummm we are......janitors!

James: Y-Y-Yeah that's right! We're just gonna get a mop to clean this place.

Meowth: That's right!

Sith Imperial trooper: Hhhhmm what's your identification numbers.

They look at each other for a moment and they think they are doomed when suddenly the doors open behind them and they turn to see Y/n, Ash ans Pathfinder as Y/n activated his light saber.

Sith Imperial trooper: Jedi!

Before he could fire he was force pushed back and slammed into the wall while the rest turn and open fire at him which he deflected the incoming shots as Pathfinder and Ash get to cover as he dashes over and cuts them down with his saber.

Pathfinder: Hello Team Rocket. Seems like we're working together.

Jessie: For now.

Y/n took out the last Sith Imperial trooper and once that slice off the controls so they will not clone anymore pokemons as Pathfinder race over to the cages where the pokemons are kepted and unlock them and they were free.

Ash: Pikachu!

Pikachu: Pika!

The two embrace with a hug while Pathfinder check on Pikachu and the other pokemon and tells them.

Pathfinder: It seems their DNA have been taking.

Y/n: Then that means they are already cloned and taking up to the surface.

Pathfinder: What should we do?

Y/n: Stopping this once and for all.

(Meanwhile)

Darth Stilk is seen in his office and pouring himself a drink when Mewtwo appears in his office and walks over to him as Darth Stilk tells him.

Darth Stilk: It seems our pokemon clone army will soon be complete. Soon every being in the galaxy shall bow down to the Sith Empire and the galaxy will be ours once again. Not to mention you will have your revenge apon the humans.

Mewtwo: Indeed.

Darth Stilk: I sense something wrong with you. Is there something you want to say?

Mewtwo:.....I want to ask that if you or your empire ever cared about the wellbeing of pokemon. After all not all were made to be soldiers of your war. What if they decide to leave after their goal is complete.

Darth Stilk: Leave? Ha! The Empire cannot accept any defection. They belong to the Sith Empire and no one else.

Mewtwo: So even after we help you rule the galaxy, you will still use us in future battles.

Darth Stilk: (smirk) Exactly. We must make sure Rebellions will not rise up and future threats destroyed. After all, a galaxy is a huge place you know. There are many others that dares to challenge us.

Then there was a beep coming from his holopad so he activated it and a hologram of an Sith Imperial trooper appears.

Sith Imperial trooper: (hologram) Sir we captured the prisoners that were trying to escape. We took them to the battle ring along with the Clone pokemon.

Darth Stilk: (smirk) Good. Hold them there. Time for them to witness our might.

(Later)

We see Green and the others backed up against the wall as Sith Imperial troopers hold them at blaster point while the clone pokemon stood behind them as Green tosses hee blaster rifle ane rasied her hands as Darth Stilk and Mewtwo appear in front of them as they walk out of the crowd.

Darth Stilk: (smirk) Now you see our might. Once we are finished with your pathetic planet, the galaxy is next and we will take over all the planet for the Sith Empire.

Misty: You'll think you will succeed?!

Brock: Whatever you do, you will fail in the end!

Darth Stilk: I disagree. These cloned pokemon are stronger, faster and more cable of battling even the strongest army's that has ever lived. Soon I will clone more and no one will not stop me.

Y/n: I don't think so sith.

They turn to see him along with Ash, Pathfinder and the original pokemons behind them as Y/n activated his twin light sabers.

Darth Stilk: You set them free?

Ash: That's right! Because they are our friends and we'll do anything to protect them!

Darth Stilk: Friends. Such a weak word for people like you. I don't need friends as long i have an army.

Y/n: Is that so? Well then, there is one more that you never met.

Darth Stilk: (smirk) And who would that be?

Y/n: The original Mew.

Then Mew appears beside Y/n which shocks everyone, even Mewtwo as Mew fly around Y/n as he turns to Mewtwo and tells him.

Y/n: Mewtwo, you were made to be a weapon but yet you have never know what it feels like to be free. I understand the struggles of being a clone but do not let vengeance get to you. Not all humans are evil.

Mewtwo: Be slient! You have no idea how it feels to be cloned and then used by others for their game.

Y/n: That is true that I'm not a clone. However I do know how it feels to be used by others. How others will use me just for their own game or something more cruel. I want you to know Mewtwo is that you can choose your own path, choose your own destiny. Don't do this Mewtwo, you can our friend.

Mewtwo looks down which Darth Stilk sees this and then shoots out force lighting towards Ash which Y/n blocks sith his saber as Darth Stilk stop shooting force lighting and calls out.

Darth Stilk: Kill them all! Let's see how powerful clone pokemons really are! Attack!

The clone pokemon charge towards the original while the original charge towards them and a large battle happened with Mewtwo battles against his original self as Mew and Mewtwo fought.

Darth Stilk watches his with a smirk on his face while Y/n and the others watched this battle happening.

Cory: This is horrible.

Nurse Joy: How can someone use Pokemon as a way of weapons of massive destruction.

Y/n: It's what they are. The sith never cares about the wellbeing of pokemon. They only care about themselves and their glory.

Ash: There has to be a way to stop this.

Brock: I don't think there is we can do. They seem they are ready to fight each other to the death.

Team Rocket also appears to see the battle going on as times gone by and the pokemon became weaker and weaker as the battle goes on while Mew and Mewtwo continue their battle until their battle sent them to the ground with a huge blast which cost the lights to shut off and all the clone and original pokemons sent flying back.

Mew and Mewtwo pushed each others away from each other as Darth Stilk watched with a large smile as the two charged up their final attack while Ash looks over to Pikachu with his clone self and then looks at Mew and Mewtwo and then rushes into the middle.

Ash: Will you two stop!

Green: Ash no!

The two pokemon fired their final attack as Ash cried out as soon he gets to the middle and moments later there was a huge bright light.

(Epic theme start)

Everyone covered there eyes from the bright light as Pikachu called out but immediately stopped mid sentence to what he was seeing. Darth Stilk watched in shock to what he was seeing while the rest look over and they stood there shocked as Ash slowly open his eyes and realised that he wasn't hit by the blast.

He then looks up and he was shocked to see Y/n with him with both of his arm straight out, holding Mew and Mewtwo's beams which shocked Mewtwo that he is powerful to stop his attack.

Then Y/n cost the beams to go straight up into the air and there was a huge explosion that cleared the sky above them, shooting down light as everyone was shocked by this as Y/n looks around and then he tells every pokemon.

Y/n: Clone pokemons and original pokemons. Why do you fight each other? Because that one of yous are clones? That some are stronger then the other? Even that is the case it doesn't mean you all battle each other to proof who is the original nor the best. At the end of the day we are all living beings living in a galaxy that has enough violence and deaths. To the clone pokemons, you must understand that you are yourselves and thus there is no reason to work along side an Empire who lack care towards you, they see you as weapons but I see you are living creatures who seeks one thing and one thing only, peace. So please, lay down your arms, embrace a life that you all were given and be part of a world of pokemon. It doesn't matter you are clones, you are still pokemons within all of us.

The clone pokemons and original pokemons looked at each other and start to make peace towards each other as Y/n watched them bounding each other and helping each other as he smiled and then turn to Ash and help him up.

Ash: (smile) Thanks Y/n.

Y/n: (smile) No problem As-

(Epic theme ends and replaced with a dual of the fates)

Suddenly he turn and blocks a incoming light saber as Darth Stilk leaps up and kicks Y/n back while force pushes Ash away and then walks towards him and swing his light saber back only for Y/n to block them and the two get into a blade lock.

Darth Stilk: I will not allow you to ruin my plans jedi!

Y/n: I'm a Grey jedi and your plans have already been ruined!

He force pushed Darth Stilk back and rushes towards him as the two dual each other while everyone watched as Darth Stilk goes on the defence as he blocks Y/n's blades only to kick him back and force push him.

He spin around and then landed on his feet and cross his two sabers together to block Darth Stilk's force lighting as he rushes towards him and reflected the lighting back at him which cost him to stumble back as Y/n kneeled him in the chin, making him stumble back as Darth Stilk was in rage and fired a powerful force push at him which he dodges and then rushes towards him as Darth Stilk slammed his hand onto the ground, creating a force lighting wave towards Y/n but he leaps up in the air as he ready his twin sabers as Darth Stilk looks up and was about block it but it was too late.

Slash!

(Dual od the fates theme ends)

Y/n lands behind Darth Stilk as he was kneel down while Darth Stilk stood behind him with his saber up to block it but the hilt cuts off, deactivating his light saber as we see a large saber slash at his chest that Y/n land on as Darth Stilk breaths heavily while he stood there as Y/n slowly gets up and deactivated his twin sabers as Darth Stilk fell onto his knees and then fell onto the ground dead.

Everyone was silent after that as Y/n turns to see Darth Stilk is now dead while Ash and Pikachu gets up to see him dead as Mewtwo goes over to him and then turns to Y/n while he turns at Mewtwo.

Y/n: You are free now Mewtwo.

Mewtwo: It seems so. Although I do not understand. Why a human like you care so much about us. We are clones after all, we are ment to be weapons.

Y/n: (smile) Not to me.

Mewtwo stared at Y/n in surprise within him but soon after he use his psychic ability to lift all the clone pokemons as they were sent flying along with Mewtwo as they make their leave.

Y/n: Where will you go?

Mewtwo: Somewhere that no one will not find us. You are a wise and powerful human. Thus I cannot take away your memories but the rest I will.

Y/n: I understand. Your secrets will be safe within me.

Mewtwo: Thank you.....Grey Jedi.

Then they fly away and seconds later there was a huge light that blinds everyone as not only they were teleported to where they were before they came to the island but their memories of this event were taking away except for Y/n's as he promised Mewtwo that his existence along with his clone pokemons will be safe in his hands.

Y/n: (smile) May the force be with you Mewtwo, always.

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