The game starts on Dagobah, where the player must find Yoda to be given a randomly generated mission on either a desert planet, a snow planet or a forest planet (or moon for that matter). Missions vary from rescuing kidnapped allies to destroying Imperial bases to finding lost artifacts. As the game's storyline and puzzle design is based around trading or using multiple chains of items, Yoda always gives the player a single item to begin with.
Star Wars Yoda Stories features a unique gameplay mechanic where the player can fly between planets in Luke's X-Wing. When exploring the world, the player will come across friendly NPCs who can give hints or trade for items, houses which can be entered, and items scattered around the world. The world is also full of danger. The player starts with the lightsaber, which, when equipped, can be used to defeat Imperial troops, Tuskens or deadly creatures.