Location: Satellite
General Grey: *sigh* Look, Giovanni, you're an idiot. Deluded with power. People have already tried the Anima Transfer Technique, and all have failed miserably. If you don't overload on power, then either Red, Gold, or I will come down there and kill you. Trust me, just give up your powers and go steal some more Pokemon.
Giovanni: NEVER! You are the fool, Grey! I am the true leader of Team Rocket! I'll prove it by blasting your satellite out of the sky!
Giovanni fires Hyper Beam at the satellite, and it gets blasted apart.
General Grey: Really? That was a two trillion Pokedollar piece of equipment! It's personal now!
Grey jumps on his Ditto Rayquaza and flies down to Mount Silver.
Location: Mount Silver
Red: ... (Venusaur stops fighting and soaks up light)
Giovanni: Ha ha! You let down your guard! Blaze kick!
Giovanni used Blaze Kick on Venusaur.
Red: (returns Venusaur) ... ... ... (fists catch fire)
Location: Spear Pillar
Operative One: Whats that boss? Giovanni's gone mad again? OK, I'll be right there. Over and out.
(To protagonists): Sorry guys, can't fight for the forces of evil today. Gotta help the General save the world from destruction.
Alcovich: Giovanni wrecking Saffron again?
Blue Cross: Nah, he's actually become a Pokemon. He tried to do the Anima Transfer Technique.
Aaron: What are you people talking about!?
Mewtwo: You'll understand when you're older. Ready to teleport?
Location: Mount Silver
Giovanni: What did you just do? Set yourself on fire?
Red: ... ... ... ... ... Well, I just did what you did. I absorbed the energy of a Blaziken, a Gyarados, a Scyther, and a Rhydon, to name a few Pokemon. I'm a pretty powerful metahuman now. Now that we're both metahumans, I can talk to you freely. Thunderbolt!
Red electrocutes Giovanni with a very strong Thunderbolt.
EDIT: Oh whoops! I didn't notice that Giovanni was on the moon!
Location: Mount Silver
Aaron: Giovanni STOP!!
Giovanni: You pathetic human! You think you can stop ME?! HA!
(Giovanni aims a Draco Meteor at Aaron)
(a Pokemon roars and Mount Silver shakes causing Draco Meteor to miss)
Red: OH MAN!! You've done it now Giovanni!
Giovanni: I know! This was my plan but you can explain it to these ignorant fools.
Red: Three years ago after I took down Team Rocket I made a discovery that changed everything. I found evidence of an ancient Pokemon. This Pokemon is the one who created the Kanto, Johto, Hoenn, Sinnoh, and Unova Regions. It ruled the Pokemon Universe without mercy. It's name is Arceus. It was said that Arceus would be awakened if and only if the ancient markers at Spear Pillar, Manaphy's Undersea Temple, and Mount Silver were activated. This is why I was chosen to guard Mount Silver, Giratina guards Spear Pillar. and Manaphy guards the Temple. (to Giovanni) The reason why most of the people who try to use Anima Transfer Technique die almost instantly. The power influx awakens Arceus just long enough for him to kill whoever is trying to become equal in power. Somehow you succeeded and now Arceus is fully awake.
(Arceus descends)
Alcovich: I have a plan. If Giovanni is a Pokemon...
Grassdragon: I see what you mean! I've been saving this bad boy for a Legendary!
MASTER BALL, GO!
The ball shook as Giovanni tried to break out.
Alcovich: Was it really that easy?
P.S. The anima transfer technique works like this: When a Pokemon dies, a human can capture its anima and gain the powers of that Pokemon through a certain technique. The joining must be consensual, i.e. the Pokemon must agree to join with the Trainer. There are ways of capturing the anima without the Pokemon dying or agreeing, though this usually results in reducing the Pokemon to a vegetative state. (Arceus doesn't like this very much.) Red's Pokemon died naturally, so he is blameless. Giovanni, however, not so much...
Location: Mount Silver
Grassdragon: YES!!! I caught Giovanni!
Giovanni (behind the protagonists): *clap clap clap* Congratulations. You have managed to defeat my substitute.
Alcovich: WHOA! Where did you come from!?
Team Rocket General Grey flew down on his Ditto Rayquaza and fires a Hyper Beam at Giovanni.
General Grey: This is for destroying my station!
Operative One: Reporting for duty General!
Operative Three: I'm here, Giovanni!
Alcovich: Now it begins in earnest...
Meanwhile, Arceus, having decided not to intervene, was watching the humans with a mixture of annoyance, humor, and sleepiness.
Location: Spear Pillar
Dialga: WHO DARES DISTURB THE MIGHT OF - Hello? Anyone there?
Palkia: Aw shoot! I was going to make this grand entrance with spatial distortions and everything!
Giovanni: Operative Three, Activate laser at will!
Operative Three: Yes, Master Giovanni. (activates laser)
All three beacons are activated simultaneously and trap Arceus in an non-penetrable force field.
Giovanni: Finally I can harness Arceus's power to control Dialga, Palkia, Giratina and all the other legendary Pokemon and rule the known universe!!!!
(to Arceus) Make Darkrai use Dark Void
Location: Some where in Sinnoh
Darkrai: Darkraiiiiiiiiiiiiiiiiiiiiiiiiii
(the world is plunged into darkness)
Aaron: No!! (to Alcovich) It's time.
Alcovich: (nods) Yes, it is.
Alcovich and Grassdragon put on their night vision goggles. Because every good trainer has a set of night vision goggles in his backpack.
Arceus: *yawn* Well? Aren't one of you kids going to fight me or something?
Giovanni: YES!!! The world is MINE!!! All the regions, known and unknown, are under my control!
Grey: Seriously? Do you even know about property laws? You don't claim possession over an area simply because -
Giovanni: SILENCE!!! Who's the metahuman controlling the most powerful Pokemon in the universe here?
Red: I am. I caught Arceus about a year back, but I let it go free. To Arceus: Right, Apollo?
Gold: Hey! I had to go withdraw some of my Pokemon from my PC. Am I late to the party?
Fortunately, Aaron knew what to do. He took out his pocket knife and started swinging at Giovanni.
Because stabbing at an all-powerful metahuman highly skilled in melee and ranged combat is totally the best thing to do.
Giovanni: You dare attack me with a knife?!? How quaint.
Aaron: (smiles) Knife? Oh you mean (presses buttons on knife)(knife extends into a full lenght sword) EXCALIBUR!
Giovanni: All right, if that's how you want to play. Operative four come in.]'
Everyone: Operative four?!?!?!?!
Operative Four: Golden armor has been recovered and Flying Fortress has been raised.
Giovanni: Good (to everyone) This has all been fun but bye! (teleports to Flying Fortress)
Golden Giovanni: ....
Red: Apollo, you can break out of that force field, right?
Arceus: It's kinda cozy in here, though... But okay.
Arceus punches the impenetrable force field, and it explodes.
Gold: Alright, Braviary, let's go to the Flying Fortress!
Grey: Wait... Where did that thing come from anyway? To Operative One: Go blow up that thing. You are the best at it.
Operative One: I'll call in Operatives Five through Ten to distract Giovanni.
Red: Wait! It looks like he's going away! He really left for real!
Leo: Aren't you supposed to be not talking or something?
Red: ... ... ... ...
Location: Flying Fortress
Sonic and Shadow the Hedgehogs: Alright, Robotnik, give back the Chaos... Whoa! Wrong fanfic!
Giovanni: Oh great. It happened again. Operative Three, get these two out of here.
Oh and by the way the world was lifted from Dark Void.
Alcovich: Is this the end of the fanfic!?!?!?
Ghestis: Not if I can help it!
Aaron: This sword is pretty heavy...
THREE YEARS LATER
Location: Aaron's room, Twinleaf Town
Aaron: Woo! Finally! I made Champion! I couldn't have become Champion without my Torterra!
Leo, a Gym Leader: If only you hadn't used so many Hyper Potions... WHAT IS THAT!
Mew appears next to Aaron and teleports him to an unknown location.
Alright, that was weak. Let me try again:
Location: Aaron's room, Twinleaf Town
Aaron: Woo! Finally! I made Champion! I couldn't have become Champion without my Torterra!
Leo, a Gym Leader: If only you hadn't used so many Full Restores...
Location: Near Twinleaf Town
Unknown Soldier: Boss, the targets are in position.
Unknown Commander: Great. Nobody's getting in our way this time around. Fire at will.
Unknown Soldier: Um boss, the guns are jamming.
Unknown Commander: What?!?
Unknown Soldier: Uh oh.
(guns explode)
Unknown Commander: What just happened?
(Mew flies by)
Location: Aaron's house.
Aaron: Now that I'm Champion, I'm going to take a long rest.
This story is over.
Guns? What are these "guns" of which you speak?
You said Fire at will so I assumed that you were talking about guns.
Location: Aaron's Room
Ace Trainer Alcovich teleports into the room.
Aaron: Whoa hello! What are you doing here?
Alcovich: I caught an Alakazam. No time to explain, can you come with me?
Leo: I don't trust you at all. (grabs Pokemon belt and bag) Let's go.
Alcovich, Aaron and Leo teleport away.
Location: Outside Twinleaf Town
Commander: They're gone!
Soldier flooded the house with smoke anyway.
Commander: What did you do that for?
Soldier: To draw attention away from us. Let's beat it out of here!