As a citizen of the kingdom of Bartonia, it's your job to discover why the Undead have begun swarming all over the world of Etheria. In this RPG hybrid you'll be following the story of your character as they rid Etheria of the Undead scourge and save Bartonia, complete sidequests for extra money, experience, items and companions, craft your own weapons and armor, capture monsters for use as mounts or to learn their spells, and even lay siege to neighboring kingdoms in order to add them to your own empire. However, Puzzle Quest is an RPG with a twist. Everything is done (as the name implies) with puzzles.

Everything in Puzzle Quest is done with puzzles. The puzzles themselves are similar to Bejeweled in execution, with a few slight variations used for things like item crafting and enemy capture.

When fighting an enemy (which can range from zombies to orcs and even castle strongholds, each with their own special spells and abilities), you both take turns using the same board. The goal is to reduce your opponents hitpoints to zero, which can be done directly by linking up skulls in rows of three or more, or by using spells which require mana. To build up mana, just link three or more runes of the same color together, just like the skulls. Every time you gain mana, it's stored in your reserves until you use it (or are hit with a mana draining attack). Gold and experience are built up in the same way, using gold coins or purple experience orbs that occupy the same board and can be linked just like runes and skulls.

The real strategy behind the game comes into play when you factor in elemental mastery (gaining extra mana when linking runes for a specific element), equipment (which can prevent damage, drain mana and more), spells (which can poison, drain mana, stun and so on) and linking up groups of four or more. The reason groups of four are important is that every time a row of four-of-a-kind is created, you get an extra turn. While it doesn't sound important, getting four runes in a row could possibly give you enough mana to cast an extremely powerful spell and give you the extra turn to cast it before your enemy can even move.

There is also a direct action mode in which players can hone their skills against various opponents independent from the story mode, as well as wireless multi-card play where two players can square off using their own characters from the campaign mode.