KS, take Loyal the Houndour. This cute little puppy wants to help you on your adventure! Aren't you lucky? But wait... something seems a little off about this little dog. It seems to have an odd affinity for darkness and pain... how strange.
Well that's because Loyal is actually EVIL! He's not loyal to you, he's loyal to CYRUS! *DUN DUN DUN!* He's evil as can be, and may only use Dark power and painful Fire type moves. Secretly he wishes to end to the world, and to achieve that goal he is tasked to tag along with you, and help you reach the Distortion World, where his plan will finally be enacted. He however won't fight any Galactic members (up to and including Cyrus). He pretends he's scared, but really, he just can't risk any tip off that might reveal his true purpose. Everything is nice and simple other than that, until you get to the Distortion World that is. In your battle with Cyrus, Loyal finally puts his plan into action, and attacks you during the battle! Because you're too busy fending him off, you may not use items while in the distortion world, and 2 of your Pokemon that aren't weak to Fire / Dark are also unable to battle, because they're too busy defending you from your own Pokemon! After you thwart Cyrus' plan and defeat/catch Giratina though, he realizes that all his efforts were for naught, and that his actions did not go unnoticed by the gods! Dialga and Palkia curse him in punishment. Dialga, master of time, punishes him by slowing down his actions. He must hold an Iron Ball at all times. Palkia, master of Space, punishes him by warping the space around him so he can never reach his opponent, meaning he can only use non-contact moves on them. He actually does feel some remorse though, and as such feels compelled to help you solo one of the Elite 4 (your choice) despite his crippled state.
Good Luck, hope it's creative enough for you. Sure the challenges were a bit generic, but I'm hoping the backstory makes up for it.