Koga's ninja manison is pretty darn cool in my opinion. In the anime it was out in the middle of a forrest. Ash and company discover it while being lost in the woods. Team Rocket also discover the gym and made the comment that it looks like a Japanese resturant. Ash and co follow Aya's tricky venonat into the gym who leads them into traps like invisable walls and voltorbs ready to explode.
The traps were inspired by the invisable walls that you run across in the game. Also in the game the gym is in the middle of Fuschsia City near their famous Safari Zone. You have to battle a lot of trainers in his gym if you don't figure out how to get around the walls.
In pokemon G/S we find that Janine has taken over the gym. She is apparently Koga's daughter. The gym is still tricky to get through. There are still invisable walls but now you have to battle a lot of trainers who look like Janine in order to find the real one.
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