40 years ago, a Celebi was being attacked by a Pokemon Hunter. Luckily, a young boy named Sammy saved Celebi. Using its Time Traveling power, Celebi transported himself and Sammy 40 years into the future. There, Ash, Misty, and Brock assist Sammy to the healing lake in the forest so they can heal the wounded Celebi. Unfortunately an evil Team Rocket member, Viscious a.k.a. "The Iron Masked Marauder", tries to capture Celebi using his technology. As Ash and Co. try to get away from Viscious, they also run into Jessie, James, and Meowth, who also want to capture Celebi. Soon it becomes a race against time to get Celebi and Sammy back to the forest before Celebi is caught and is used to destroy the forest and themselves. 

(Source: ANN)

As they continue their journey through the Johto region, Satoshi and his friends visit Altomare, an island city that hosts an annual racing event called the Pokémon Water Race. While Takeshi and Kasumi are enjoying themselves, strange things seem to be happening to Satoshi—he somehow loses the water race, sees some women attack a girl with their Pokémon, and despite them saving her, the girl later denies ever seeing Satoshi and Pikachu before!

Fortunately for Satoshi, his confusion clears up as he learns that the girl he and Pikachu saved earlier was actually a Pokémon named Latias, who likes to disguise herself as her human friend, Kanon. Latias and another Pokémon, Latios, are known as the Eon Pokémon, as they inhabit and guard Altomare along with a mystical blue sphere called the Soul Dew. An ancient legend of Altomare is highly connected to the Eon Pokémon and the Soul Dew, and is well known among the locals—as well as among Latias' earlier assailants, the thief sisters Zanner and Lyon. As the thieves attempt to capture both the Eon Pokémon and the Soul Dew, Satoshi is forced to act in order to stop them from bringing disaster to Altomare.

[Written by MAL Rewrite]

This is the 6th Movie.

Satoshi, Haruka, Takeshi, and Masato come upon the festival of the Wishing Star of Seven Nights. During their enjoyment, the legendary pokemon, Jirachi, decends from the heavens and befriends Masato. 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

(Source: ANN)

Satoshi and his friends travel to LaRousse, where they meet a boy named Tooi who is afraid of Pokemon due to an incident that happened four years earlier. Meanwhile, Deoxys, a Pokemon from space, has reappeared, putting a barrier around the city and kidnapping people. Rayquaza, a Pokemon that lives in the atmosphere, comes to fight it.

(Source: ANN)