Professor Oak will be encountered later in the series. He will live in pallet town, although he will be named many times throughout the story before. When he will be encountered with, it will be revealed that people refer to Gary now when they talk about professor Oak, since he has taken up the title as well as his grandfather's laboratory.
Gary will now live in Pallet, training with his pokemon but refusing to let go of his grandfather, so he put his trainer days behind him and focuses both on his research and taking after his grandfather. In Pallet, now an almost abandoned city due to a corrupted bird living nearby (either moltres or articuno), Gary lives with Samuel Oak, Delia Ketchum and his sister. He and his sister take after the elderly. When Vergil goes to Pallet, his father's hometown, he gets to know the city and gets gary to aid his father. He and Gary get close, and somehow Delia, Sam and Gary's sister are killed when he and Vergil go out on a mission. Gary is ruined over this and says his siter was a strong trainer and there is no way this could have happened, and decides to take revenge by aiding Vergil and Ash at retaking Saffron, and eventually Lavender. He is among the ones betrayed in Saffron, and his fate is unknown after the battle