The story starts with four wild Pokemon living in a big city — Jet the Buizel, Fingers the Aipom, Sparks the Pichu, and Kori the Sneasel — meeting to escape from a gang of Poochyenas. Along the way, they meet a couple of creepy street merchants, several gang leaders, a paranoid Sandile, and an Arcanine with a mysterious gift for Flint. Then all of their gangs get in a fight with a different gang made up of felines. Kori gets kidnapped by the Claw Gang, and everyone else tries to get her back, doing such things as finding an underground nightclub and entering a tournament to get information from a Porygon Z.
The gang then splits up, either joining different gangs or going off to pursue new plot points. The Big Bad(s) have also been introduced, in the form of a group of Dragon-type Pokemon that want to conquer the city, led by a Dragonite.
Wild Pokémon in the Big City contains examples of:
- In-Series Nickname: Lickitung is "The Tongue of Arceus".
- Knowledge Broker: Paul the Psyduck trades on any sort of stuff, such as bad memories.
- Make Me Wanna Shout: Absol uses Roar to finish Jet.
- New Powers as the Plot Demands:
- Razor tells Liepard to use Dream Eater on Kori, which would normally not affect her due to her typing. The players decide to let it happen anyway.
- Liepard also has more than four moves, which is the limit for all the other characters.
- A few moves are used differently than they would be in the games, such as Absol using Roar as an attacking move.
- Running Gag:
- This Is Gonna Suck: Pretty much everyone when Lickitung starts fighting outside the match cage.