Fierce Battle in the Monster Ball Factory! Pikachu VS Nyarth!! - S18-E34
Revealing mistake: When Ash and his friends put all their Poké Balls in the case, Bonnie's hands are briefly drawn like Clemont's. (00:03:04)
Fierce Battle in the Monster Ball Factory! Pikachu VS Nyarth!! - S18-E34
Revealing mistake: After Pikachu points to Ash's friends, Ash's left hand passes through him. (00:17:39)
Answer: He is a good guy but just found himself in a bad situation when he worked for Lysander. He didn't want him to harm Ash and his Pokémon when he was trying to get the special bond between Ash and his Greninja to work. He does leave Lysander and go back to being a good person.