The Fuchsia City Gym is riddled with invisible walls and trapdoors, which have been built up over the years from its long history as a ninja stronghold – and rearranged or added to whenever there was a suspected leak of its layout – whether from capture, torture, or simply defection to an enemy daimyo. The age of human ninjas needing to use their skills in combat here has long since passed, but the ninja pokemon of the gym – trained by a man known to most only as Koga, the name of the clan he heads – have carried on this centuries-old tradition in pokemon battles.

Koga's pokemon are drilled not only in the use of the clan's immense catalog of poisons, but also in the gym's own layout, which they use to disappear from the battlefield entirely when badly wounded, denying their foes a precious knockout. An elaborate network of tunnels under the gym leads these pokemon back to their own pokeball in Koga's bag, from which they emerge, fully rejuvenated, to rejoin the match – if it lasts long enough.

Although few of Koga's pokemon hit hard with their own attacks, they still challenge trainers through their disappearing act and the slow attrition of their foes from poison. His clever techniques drive many opponents to extreme frustration, but Koga has little answer for raw power; those who earn the Soul Badge are typically those who train their pokemon to hit hard enough to knock out their foes before they have a chance to exploit their ninjutsu. Challengers should note that the trapdoors do not cover all the Fuchsia City Gym, and the invisible walls can at times stall Koga's pokemon as well as their own; some trainers defeat Kanto's top shinobi through accidental positioning and simple luck.