Pikachu's Vacation (ピカチュウのなつやすみ, Pikachū no Natsuyasumi, Pikachu's Summer Vacation) is a 21-minute short film that is shown before Mewtwo Strikes Back in both the theatrical, VHS and the DVD version of the main film. It is the first of the "Pikachu shorts" in what would be a traditional process of hosting a 20+ minute mini-movie before the main Pokémon feature that would last up until the sixth that would follow, focuses primarily on an action-packed affair involving solely the Pokémon seen from the anime as they take part in a scenario that eventually illustrates a moral.

In Pokémon fan communities, Pikachu's Vacation was noted for introducing the never-before-seen Pokémon character Snubbull, as well as the first primary anime appearance of Marill. This became a tradition for all Pikachu shorts, as they were used to introduce new Pokémon from the upcoming "generations" of Pokémon games, cards, and anime material.

Mewtwo Strikes Back

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.Shortly afterward, he meets Giovanni, the head of Team Rocket, who proposes a partnership with the Pokémon in exchange of helping him control his 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. After defeating Giovanni, Mewtwo flies back to the island where he 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.