Story Mode was the original content for ''[[Magic: the Gathering Puzzle Quest]]''. It is where all players start out and is a good way to learn the mechanics of the game and earn some basic rewards to prepare for [[Events]].

Rewards are earned for the initial win, for winning once with every color, and for winning with different optional objectives. Winning with a colorless planeswalker does not advance the "win with every color" objective.

Story Mode is split between four levels. Each level has at least 4 chapters, and each chapter has up to 16 battles.

The Training story features short chapters with easy battles to introduce players to the new mechanics of specific [[Card set]]s. Many Training chapters provide as rewards [[Cards]], and in some cases [[Card pack]]s, from the corresponding card set.

The Battle for Zendikar story features a tutorial (similar to Training) plus further chapters of increasing difficulty. The enemies' cards consist of mostly BFZ cards, and some Origins cards.

Heroic Encounters feature a set of relatively high difficulty story battles, corresponding to the five basic planeswalkers. Each level starts with the enemy getting some sort of advantage in the form of creatures and/or supports that are in play before the battle begins.

* All rewards in a single Story mode battle can be earned in two games. To do this, you would meet the two optional objectives in addition to using a three -color walker (such as [[Nicol Bolas, God-Pharaoh]]) on one run and an opposing two -color walker (such as [[Huatli, Radiant Champion]]) to meet all five color objectives.