Ash, May, Brock, and Max come upon the festival of the Wishing Star of Seven Nights. During their enjoyment, the legendary Pokemon--Jirachi, descends from the heavens and befriends Max. Jirachi, with the power to grant any wish, is sought after by many people wanting to claim its power. One man seeks to use its legendary power to revive an ancient Pokemon known as Groudon, unaware of the dangers hidden within Jirachi's powers
Jirachi is captured and tortured by the villain, and screams for a long time.
Many of the main characters are eaten, and are shown in bubbles in the belly of the monster, also screaming in fear.
Jirachi is restrained and tortured. Absol is put in a cage. Team Rocket tries to capture Pikachu, and puts it in a little clear ball. As well, Kirlia and Mighteyna are captured in a cartoonish net.
Brock isn't canonically black, but lots of American audiences see him this way. This is important to note because when he dresses as a clown, he gets the red lip overdraw. Since he's darker skinned, this can be alarming. It's for one scene and then he's back in his normal outfit for the rest of the movie.
A tracking device is put on the bottom of the car Diane and the kids are leaving with. Team Rocket also does their usual snooping via balloon and binoculars.
Seviper is featured in the closing credits. Tendrils try to eat the characters, and one of them even grows a mouth and hence looks very snake-like. There may be some additional snake Pokemon cameos.
At the beginning of the movie, Team Rocket is dressed as clowns in several scenes. In some scenes in the middle, Ash and Brock dress as clowns as well in the same costumes.
Diane and Butler both sacrifice themselves to stop others from being absorbed by the goop tendrils. Diane jumps in front of Butler, and Butler stands deliberately in front of Jirachi, Max, and Ash.
There are a couple scenes where people fall from high places, off of structures etc, but they are always saved in time. The worst that happens with falling is Butler who is visibly afraid as he falls, but is saved by Salamence.