Game is managed via the obj_game object, as well as the game_variables variables, which control when certain events occur in the game. Different systems like battling, puzzles, and menus are in different rooms as well.
Download all files, or just the .yyp file, and build through GMS2.
Story could be more fleshed out in future iterations, as well as additions to things like sound FX and other visual/audio design pieces.