Team Rocket discuss avoiding romantic relationships with the opposite gender, which is referred to via the use of "sex" multiple times. Meowth comments teasingly that Jessie and James don't need relationships as they have each other.

Throughout the film, Melody teases Misty regarding her relationship with Ash, asking repeatedly if they are dating and encourages them to sort out their issues if they get married. Misty blushes with each of Melody's quips, actually having a crush on Ash.

Melody kisses Ash on the cheek and very mildly flirts with him.

Misty, Melody, and Jessie all wear outfits that show their midrifts, though there is nothing sexually inclined about it.

Moltres, Zapdos, Articuno, and Lugia are all enormous birds that possess elemental powers (fire, lightning, ice, and psychic-based powers).

Moltres and Zapdos are individually captured in cages that electrocute them into paralysis.

The characters are caught in violent storms several times, though no one is hurt apart from being thrown around in their respective ships.

Team Rocket's submarine crashes into a cliff face though it is done for comedy and they survive.

Moltres and Zapdos destroy the villain's aircraft, causing it to crashland on an island, though all of the characters survive.

Zapdos and Pikachu strike each other with electricity as a form of communication.

A helicopter crashlands but all of the occupants survive.

Lugia is struck by lightning and falls into the ocean, but is revived minutes later. Later on, Lugia is electrocuted by the villains' capture cages, and fires an energy blast that wounds Moltres and Zapdos, before he plunges into the sea and is knocked unconscious.

Articuno is wounded by Moltres and Zapdos, smashes its head against a stone shrine, and is knocked out.

Team Rocket throw themselves off Lugia and fall into the ocean, but survive.

Ash is thrown into a lot of peril during the film, and is knocked unconscious at one point.

Lugia being injured may upset younger viewers.