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Gino Giovanni, an extremely rich man who owns his own castle, notices the strength of the Pokémon species and decides that he shall capture them and use them as slaves to perform tasks for him. As such, Pokémon slavery becomes a common thing throughout the region of Orre. The Fiore and Almia regions, however, who had long treated Pokémon as friends, were angered at Orre and as such a war began between the two regions. During this period of chaos, the rulers of Orre mysteriously died and as such Gino stepped up to fill their spot.
Ishmael, a young boy who lived in Orre, had parents who worked on a plantation. They themselves used Pokémon as slaves; while Ishmael was a young child, he became a friend with a small Caterpie that worked for his parents. Gino had made a law stating that if not enough crops were grown and 25% of them were given to the government, then the punishment was death. As such, Ishmael's parents were killed by Gino. Ishmael, who was now grown up, set out with Caterpie to kill Gino and gain his revenge.
As Ishmael infiltrated Giovanni Castle and went into the room Gino was in, Gino grabbed Caterpie and shot him with a musket, killing him. This causes Ishmael to become extremely angry and he finally realized that he wasn't doing this just for revenge; he wanted to save the Pokemon as well. So, Ishmael and Gino had a fight to the death and eventually Ishmael won. As Ishmael freed the Pokemon from slavery and also freed Orre of Gino's rule, Arceus appeared before Ishmael and congratulated him on doing a good job. Ishmael then fades away into light.
As the credits show, Ishmael and Caterpie can be seen walking through the clouds together.
- Bone Club (dropped by Cubone or Marowak)
- Blastoise Cannon (dropped by Blastoise)
- Vine Whip (dropped by Bulbusaur, Ivysaur or Venusaur)
- Leaf Shurikens (occasionally dropped by Grass Pokemon)
- Seed Gun (crafted from Blastoise Cannon and Bullet Seeds)
- Coconut Cannon (crafted from Blastoise Cannon and Coconut Faces)
- Arrow Claws (crafted from Wood and Zangoose Claws)
- Poison Axe (crafted from Seviper Tail and Wood)
- Poison Knife (crafted from Seviper Fang and Wood)
- Coconut Faces (dropped by Exeggutor)
- Wood (dropped by Tree-Pokemon)
- Bullet Seeds (dropped by Bulbusaur, Ivysaur or Venusaur)
- Zangoose Claws (dropped by Zangoose)
- Seviper Tail (dropped by Seviper)
- Seviper Fang (dropped by Seviper)
- Telekinesis - Pick up and move objects and small enemies
- Pyrokinesis - Set enemies and objects on fire
- Cryokinesis - Freeze enemies inside a block of ice
- Distortion - Causes various random effects
- Aerokinesis - Knocks enemies backwards with a strong gust of wind
- Electrokinesis - Causes a lightning bolt to hit an enemy or object
- Magnetokinesis - Causes all enemies and objects to move towards a certain point
- Clairvoyance - Shows an enemy's weaknesses and strengths, as well as their remaining health and a short description of them
- Neku - Sends sound-waves to attack the enemy
- Tackle - Causes damage to and knocks an enemy back
- String Shot - Slows an enemy down
- Bug Bite - Causes damage to an enemy and restores Caterpie's health slightly
- Metapod - Metapod acts as a shield to Ishmael for a few seconds, capable of reflecting all projectile attacks and blocking melee attacks
- Charizard - Flies past and breathes flames on the strongest enemy on the screen, causing them damage and making them set on fire
- Jigglypuff - Causes all enemies on the screen to fall asleep, except for those resistant to sleep