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Indigo, after failing to achieve a career as scientist, was trapped in the Amerikan Kingdom. He watches in the distance, seeing Fandro (his brother) and Doh get married. In disgust, Indigo returns to creating obscure inventions. Eventually, through hacking and breaking the laws of physics, he manages to get a Pokémon out of his game - a male Gardevoir. With Gardevoir's smart mind and care for Indigo, the young scientist decided to show all his envy on Fandro. Ten minutes after the wedding ended, Indigo and Gardevoir lay a mass attack, killing everyone except for Fandro and Doh, whom escape from the onslaught. In revenge, Indigo creates a robot army called The Fusionbolts. The Fusionbolts are robots based upon Swamperts and Mudkips. He sends these to end Fandro and Doh.
One night, Fandro hears a strange noise outside of his home. He looks out of the window and sees an army of Mudkip-like robots outside of his door. He wakes up Doh, and together they fight the robots. Figuring it must be Indigo, they search for his base. Upon getting there, they get hit by a mysterious psychic force (Gardevoir) and they both fall unconscious. They wake up in an odd forest surrounded by more robots. Fandro and Doh fight these, and manage to survive, but barely. After hours of searching, Fandro and Doh realize they are nowhere near home. At first they decide to give up, until a guy named Claus helps them escape the forest, and they find themselves in a huge city called New Fusionbolt City (originally named Old Pork City), which has also been taken over by the Fusionbolts.
Doh asks Claus where the fastest possible route to their (and Indigo's) hometown, Roseradeisthebestpokemonevercreateditissobeautiful, and oddly, it is extremely far away from Fusionbolt City. They also tell Claus about the mastermind behind these creatures, Indigo. He tells them that he and Gardevoir have become the monarchy of the Kingdom, ruling over the entire country. Fandro, Doh, and Claus agree to team up to defeat Indigo and bring peace to the Kingdom. However, the trek to his castle is long, as his castle is in the Indigo Empire, which is several hundred miles away.
After going through several levels without much plot, comes the end of the game.
Fandro, Doh, and Claus reach Indigo's castle, which is guarded by several Swampert Fusionbolts. They fight them and win, although the door automatically opens, and they see Gardevoir. Claus tells Fandro and Doh to sneak past Gardevoir while he deals with him. In the castle, they encounter Indigo, who has now gotten much powerful due to various inventions. Fandro and Doh try to fight Indigo, but they both lose to his powers. Indigo then captures Claus, and turns him into a cyborg known as the Masked Man while he is unconscious.
Fandro and Doh wake up to realize they are in a cage in a room patrolled by a mysterious masked man. Fandro realizes that he has an OP Mega Heracross, which he sends out to destroy the cage. The Masked Man attacks Fandro and Doh, but using Arm Thrust, Heracross manages to tear his mask off, revealing that it is really Claus. Because he turned good after the removal, Claus decides to go after Indigo with them. By Indigo is a huge army of Fusionbolts. Fandro sends Mega Heracross to attack Indigo, and Claus sends out his OP Mega Kangaskhan, and they both beat up Indigo while the humans defeat the Fusionbolts. Eventually Indigo gets defeated by the Megas, and he gets arrested, and the world turns back to normal.