How does this sound?
Giovanni creates a device capable of completely controlling Mewtwo as well as multiplying its power exponentially. Then he finally makes his position as head of TR known to the entire world in a hostile takeover. Ash realizes that because he is one of Mewtwo's few (known) human friends, he may well be able to get through to Mewtwo and stop Giovanni.
Knowing that he can't go at it alone, Ash calls in all of his other friends (not every one he's ever met; just the one's who have been in the main group and some of their rivals like Barry, Kenny, Gary, etc.). Ash and his group reach a large tower made by Giovanni, but are met outside by every other member of TR at the door. A large brawl ensues, and the good-guys quickly realize that they are too vastly outnumberred.
Suddenly a large plane touches down and the fighting stops as everyone looks at it in astonishment. The door opens and a man who has never been shown before walks out. He introduces himself as Ash's father, and tells Ash that Delia had contacted him after hearing of what was happening. Some members of TR start commenting "so you've got one more guy" "we've got plenty more pokemon" and "come on, how are you gonna win with just one more guy?"
Ash's father answers by asking them "who said it was only one more?" He points at the plane and a gigantic side hatch opens, revealing all of the gym leaders and Frontier Brains from every region. TR starts feeling a little less confident, but they continue to fight. The heros notice thatthey are now evenly matched, not ahead; so Ash's father tells him to sneak into the building while the rest of them are occupied. Ash does as he is instructed and rushes through the door. He is met by Jessie, James, and Meowth; who tell him that they were assigned to guard the stairs in case anyone tried such a tactic.
Pikachu hits them with a Thunderbolt and Ash runs past them as they stagger back up. They chase him up the stairs until he reaches the top floor, where Giovanni and Mewtwo are waiting. Giovanni angrilly says to JJ&M "you fools! I can never count on you for anything!" Ash looks at the now cowering JJ&M and asks them "that's the guy you've been working for? why do you help him if he doesn't even respect you?"
JJ&M realize now that ever since they started chasing Pikachu Giovanni has given them zero respect or recognition; it is time for revenge. They announce their resignation to Giovanni and challenge him. Giovanni laughs as a door opens and Mewtwo emerges. Ash immediately commands Pikachu to use a Thunderbolt on a device on Mewtwo's head, presumably the control device. When it hits a puff of smoke shoots from the machine and Mewtwo goes berserk. Giovanni asks Ash "do you realize what you've done? Now he's still furious but I can't control him. Thanks to you Mewtwo is going to go on an uncontrolled rampage!" As Mewtwo stands back up, he blasts open the back wall and flies away as Ash rushes up and grabs hold of his tail. Giovanni tries to give chase, but is stopped at the door by JJ&M, who tell him that they still wish for a battle.
As Mewtwo drags Ash higher and higher, Ash continues trying to talk to him and Pikachu keeps blasting the device; but Mewtwo is too angry to listen and the device refuses to budge. Mewtwo stops and uses his psychic powers to Throw Ash and Pikachu off. As Ash plummets to earth, he thinks to himself "this is it. I've failed. I couldn't do anything to stop Mewtwo. Sorry, my friends," but before he hits the ground an orange blur rushes beneath him to catch him. He looks down and realizes he is now riding Ho-oh. Ho-oh soars back up to where Mewtwo is and confronts him. An epic battle ensues, ending when the heavilly damaged Ho-oh uses Sacred Fire on the device. The device finally breaks and Mewtwo regains his mind. Both Mewtwo and Ho-oh begin to fall from the sky, with Ash and Pikachu still on Ho-oh's back. As they are about to land, a bright light hits them, they stop in midair, and the booming voice of Arceus echoes down from the heavens and tells them that he chooses to spare their lives as a reward for their great deed (except Mewtwo; he is saved because he had been forced to endure such madness). Arceus then appears at the site where JJ&M have just beaten Giovanni. He looks at Giovanni with great anger and says "you dare harm the balance of nature and threaten the fate of both humans and pokemon. For that you shall recieve the full force of my wrath. JUDGEMENT!" A powerful Judgement attack slams down on Giovanni, who the vanishes, seemingly vaporized.
After everyone goes home and the rest of TR disperse and/or get arrested, Ash and his family are together at their house. A long conversation takes place, and Ash tells his parents that he is still sad that he never became a pokemon master in the pokemon league. His father looks at his and says "son, one tournament will never be able to give you the name of a master. You have done that on your own. Today, you are a pokemon master!" Ash then tells his father that he has one more request before his father leaves again; a battle. The two meet outside the next morning and Ash's father reveals his main pokemon, a Raichu. Pikachu and Raichu rush at each other with Volt Tackle and the final episode ends in a epic freeze-frame of the impact.
