There's a base in a bush right outside Fortree City (route 120, the route to the right). It's the first bush you come to; basically you go down as soon as you get to the tall grass and there's a bush at the top of the cliff, just over from the steps down to the water. It's not a very interesting shape inside - it's kinda two rectangular shapes joined by a little path in the middle - but I'm sure it's one of the most spacious secret bases.