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Story Modes are phases in the Muffin Knight and there are currently five modes. At first there was only one mode but more were added in an update. To unlock the next mode, you must defeat the Lava Lord. When you unlock a new mode your skills reset. However, you can swap between modes at any time.
Knight Mode is the first mode and is completely basic.
King Mode is the third mode. In this mode stages are more difficult and the Graveyard will receive a new look. Playing in King Mode grants a 20% experience bonus.
Dark Lord Mode is the fourth mode. You must get many, many more muffins to unlock stages.
Emperor Mode is currently the fifth and final Mode.