Gameplay sum up: You begin in Rogue Port, a hub that leads off to the game's 7 chapters. Rogue Port also has many useful facilities, including a shop where you can buy health and items; an inn to sleep and regain your health; a fortune teller to give you hints on where to go and what to do next in the game; and a save block to save your game—there are many more cities scattered between levels with the same facilities. Your objective is to find and collect the 7 Crystal Stars. To do this, you will explore the side-scrolling levels, solve puzzles, fight enemies and talk with characters. Mario will also gain powers to counteract the ever increasing complexity of environments, like turning into a paper boat and floating across water, becoming razor thin to pass through tight spaces, flying in the air as a paper airplane, and more as you progress.

The combat system is what you call turn-based, typical of the RPG genre. What this means is, when Mario (and party) come across an enemy, the game takes you out of your current environment and places you on a stage, with Mario (and party) on the left, and the enemy on the right. You then have the option to pick commands from a menu, like jump, which will have Mario jump on the enemy's head; hammer, which will have Mario attack the enemy with a hammer; item, which will have him use an item to restore health or use power-ups; or Tactics, where Mario can either defend himself for the turn or flee the battle. Once you choose, Mario will automatically perform the selected command, and return to his starting position. Enemies will then take a turn, and attack Mario—you wait for your next turn and repeat, until the enemy is defeated.

After defeating enemies you receive Star Points, and when you've acquired 100 Star Points, you will level up, which, in turn, will increase your total health and combat skills. In addition to leveling up, you'll come across Badges, which can be equipped and used to boost specific skills for use in combat. Throughout the game, you'll come across certain characters who will join you on your journey. These characters have specific abilities in battle, and you'll sometimes have to use their unique abilities to destroy the enemy. These abilities will also be used in levels and are required to progress further, including abilities like: Bobbery, who is an actual bomb, and can be used to destroy barriers blocking your path; Koops the Turtle, who can use himself to spin in his shell as to reach normally unreachable objects like items and switches, etc.