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The show's production manager uploaded the whole thing starting here.
He also uploaded instrumental versions of the entire soundtrack starting here.
The costumes and puppetry are very good, especially the puppets.
"You and Me and Pokemon" has every single Pokemon the show made come out to dance with the human cast. This scene was used in all the commercials.
Giovanni built MechaMew2 all by himself.
MechaMew2 is seemingly unaffected by any attack, no matter how strong.
As crazy as Giovanni's plan sounds on paper, it actually works. He gained every type of Pokemon attack on Earth and defeated everyone that challenged him.
Giovanni's song "It Will All Be Mine," featuring a performance by Darren Dunstan—who would later VA Pegasus in Yu-Gi-Oh!—and marching Rocket Grunts. Jessie and James also recite their motto and make it sound threatening.
Giovanni: Some things don't have to change. Delia: Yes, they do. I've changed.
The end of Giovanni's reprise of "Everything Changes," while cool on the soundtrack, is awesome on stage due to the helicopter sounds.
Team Rocket finally captured Pikachu and delivered him to Giovanni. Jessie and James had to pick Ash's Pikachu out from a crowd of other Pikachu dancers. They eventually waited for him to dance near them, then hauled him off in the Magikarp submarine.
James tells Pikachu to "do that thunder thing you always do to us." He does, and shocks every Rocket in the room and frees Delia and Professor Oak.
Team Rocket was sent to capture Ash when Pikachu wouldn't obey their commands, but when Ash learned what happened to Pikachu, he ordered them to take him to Giovanni.
When Giovanni says Delia made a big mistake when she walked out on him, Ash responds that it wasn't as big a mistake he made by stealing his Pikachu.
While the Pokemon battle between Ash and Giovanni is short, it was the closest they'd come to a fight until the Best Wishes anime series 13 years later—and in the anime, their fight was even shorter.
When MechaMew2 defeats Pikachu, Ash tries to fight Giovanni himself. With his fists. In song. Giovanni responds in kind.
Giovanni: Thank you, Ash Ketchum from Pallet Town! Now nothing can stop me! Ash:[charges forward, fists raised] I can, and I will! [cue "You Just Can't Win" as Rocket Grunts surround Ash]
During the fight, Giovanni tries to punch Ash, who dodges and taunts him about it.
Ash: Guess you're slowin' down, old man; can't hit what you can't catch!
Later in the fight, Giovanni grabs Ash by the chin/neck, lifts his head and shoves him away, then goes into a Badass Arm-Fold.
Giovanni tries to just kill Ash and Pikachu with Hyper Beam after they served their purpose in his plan. If not for Mewtwo's intervention, he would have won.
Mewtwo blocks MechaMew2's Hyper Beam with a force field.
Mewtwo defeating MechaMew2 by teaching it compassion, courtesy of Ash's memories and pure heart.
MechaMew2 gains sentience and learns right from wrong, puts Giovanni in a headlock, and gives a touching speech just before blowing itself up.
Giovanni: I didn't give you the power of speech! MechaMew2: You didn't give me a lot of things, but you did give me the ability to learn. And I have. From the boy, I've learned about love and goodness. His heart is pure. His love for Pokemon and his friends and family is real. I've learned right from wrong, and I've learned which one you are. Now I know what I must do. Something else I learned... Self Destruct.
Giovanni gets some points for actually surviving the attack.
In the Finale, Giovanni comes out with smudges all over his face and suit and glares at the cast, until the heroes invite him to dance. Albeit reluctantly, he does—and tries to dance with Delia, but Professor Oak interrupts him with a karate chop.
The Finale has every member of the cast dancing with all the Pokemon, including Team Rocket.