In Magi-Nation, the player takes control of a boy named Tony Jones who is dared by his friends to enter a spooky cave. After finding his way in he gets lost and finds a magical world inside called the Moonlands filled with many magical creatures. Now he must fight his way back to the mouth of the cave and escape back to reality.
The gameplay is a mixed blend of many types. The main gameplay is in the style of an RPG such as Final Fantasy, where the player explores the world, encountering enemies to fight, locating treasures and relics that can be used in battles, and talking to other magical creatures to help find clues to escape.
The battle sequences are a blend of Pokémon and Yu-Gi-Oh!. The player battles enemies using a turn-based card system with captured monsters from previous fights, and can use certain relics scattered throughout the world to combine with their monster/card to help them defeat enemies and advance. However, there is only a certain amount of relics so the player must use careful strategy when using them in battle.
