Pokemon - The First Movie

SYNOPSIS via Wiki:
The Pokémon Mewtwo was created in an island laboratory from the DNA of Mew, a rare Pokémon believed to be extinct, recovered from fossilized remains. Displeased with the concept of being nothing more than a mere lab experiment, Mewtwo destroys the laboratory[2]. Shortly afterward, he meets Giovanni, the head of Team Rocket, who proposes a partnership with the Pokémon in exchange of helping it control its powers. Mewtwo is "trained" over the next few months, being pitted against challengers in Giovanni's gym and restraining Pokémon for Team Rocket to capture. Mewtwo eventually realizes that Giovanni is merely using him as a tool and destroys his headquarters. Mewtwo flies back to the island where it was created and begins plotting revenge against humanity.
Meanwhile, Ash Ketchum and his friends Misty, Brock, Pikachu, and all their Pokémon companions receive an invitation to a party hosted by the world's "greatest Pokémon Master" on New Island. Ash and his friends are excited and rush to the docks in an attempt to catch a boat to New Island, but a storm is mysteriously formed and all boat rides to the island are canceled. Undeterred, several trainers make their way out to the island by riding their Pokémon, though neither Ash nor his friends have any Pokémon of their own that can help them safely navigate the stormy sea. In their latest plot to steal rare Pokémon, Team Rocket offers the trio a lift to the island, disguised as a pair of Vikings, but their small wooden boat is destroyed by a wave. Ash and his friends manage to reach the island with their aquatic Pokémon, and are escorted inside the palace on the island.
Mewtwo reveals itself to Ash, his friends, and three other trainers who braved the storm battle as the "World's Greatest Pokémon Master," and that it had created the storm with its powers to test the trainers' wills. After being berated by Mewtwo for the relationships they share with their Pokémon, Ash and some of the other trainers challenge Mewtwo after witnessing Mewtwo's confession of having kidnapped Nurse Joy for his own personal purposes, the trainers pits their Pokémon against clones of Venusaur, Blastoise, and Charizard. The clones easily defeat the trainers' Pokémon. Mewtwo proceeds to steal everyone's Pokémon, including Ash's Pikachu, with a special set of Poké Balls; he also captures three trainers with these Poké Balls as well. Ash pursues his Pokémon as they are taken deep into a cloning facility on the island and rescues them while they are being cloned. The clones join with Mewtwo and the cloning machine explodes, releasing all the captured Pokémon. Mewtwo announces its intentions to overthrow humanity with its army of Pokémon and rule the world. Enraged, Ash lashes out at Mewtwo, who repels and blasts him away with its psychic powers. Ash is saved by Mew, the rare, playful Pokémon having appeared periodically before, who is engaged by Mewtwo. A brutal battle between the trainers' Pokémon and their clones erupts, although Pikachu refuses to fight with its own clone.
The trainers are unable to bear this senseless violence, even while the two sides grow fatigued and Mew and Mewtwo continue fighting. In an attempt to put an end to the ordeal, Mew and Mewtwo sum up all their remaining powers for one final duel. As they open fire however, Ash runs to the center of the arena in a brave but desperate attempt to stop the fight. Ash is turned into stone in the attack, and he collapses in the center of the arena. Pikachu runs to the side of its now-deceased trainer. After trying to get him off the floor, Pikachu attempts again using Thunderbolt, but in vain. In its grief, Pikachu starts crying for its fallen master, the other Pokémon in the arena doing the same (Team Rocket's Meowth and his clone also do the same). The tears reach Ash, their mystical healing powers reviving him. As everyone rejoices, Mewtwo, taken aback by Ash's act of selflessness to save all the Pokémon, has an epiphany over the relationship between humans and Pokémon, and realizes that the circumstances of how one is born should not be allowed to divide anyone. It leaves the island with Mew and the cloned Pokémon, erasing everyone else's memory of the horrifying incident, knowing it is for the best.
Ash and his friends find themselves back on the docks with no idea how they got there. Ash looks up to the sky and spots Mew flying past, and recounts to his friends how he saw a rare Pokémon on the first day of his journey.