>>42237813Team Ion, an anti-Pokémon Team who seeks to rid the world from Pokémon forever. They plan to develop a "final solution" to the Pokémon problem. Unlike previous teams, they don't fight with real Pokémon. Instead, they fight using manufactured copies of the real ones.
Their final solution is the development of a "Machine Arceus" to get rid of Pokémon forever, but it immediately backfires as their most powerful creation turns against them and plots the destruction of both humans and real Pokémon. The reason is what we already know: technically speaking, humans are Pokémon too.
The Machine Arceus destroys much of Team Ion, except for its leader. Their boss helps MC in the battle by revealing the weak point of "Machine Arceus", but he ends up "killed" during the fight by a stray energy blast.
Machine Arceus's body is destroyed beyond repair, but his digital consciousness enacts an emergency plan: possessing the MC while he is distracted by the "death" of Team Ion Boss.
The final fight of the game involves the MC's spirit fighting a Pokémon battle against the usurper trying to take over his body, a battle against your own pokémon team vs a pokémon team you can call from inside your box.
The MC wins the battle and recovers control of his body, erasing Machine Arceus's digital consciousness from existence.
An after-credits call reveals the Team Ion Boss is not dead, he faked his death after concluding his true mission: fueling the flames of hatred inside Pokémon. He hopes their collective hatred for humans will one day grow strong enough to awaken the true form of a Legendary Pokémon that is none other than himself.
Postgame is going after this evil Legendary Pokémon who feeds on hatred, doing a pilgrimage to receive the blessings of different Legendary Pokémon and gather enough followers to fight against him. Meanwhile, the player must stop hostilies between real Pokémon and humans triggered by the conflict with Team Ion.
