did you go to the Washroom and get fixed up? also if you go to far down one path or the other it'll lock the opposite path.
I would go to every room leading up to where you get the axe then go back to where Makoto is. Once I rescue her and try to go back to the ladder, a dialouge box saying I still need to rescue her appears.
I did go to the washroom after resueing her but nothing seemed to happen. Unless I'm not clicking on the right area?