A new feature added to New Mystery of the Emblem is the addition of My Unit. My Unit is a customizable character that the player controls during the game. The player can choose the My Unit's name, appearance such hair style, colour and accessories such as an eye-patch and also the class of the My Unit.
The My Unit will also be able to talk to other units to get hints and tips for the game. The game also includes 7 new prologue chapters not in the original to introduce the My Unit to the story as well as new chapters later in the game revolving around the My Unit.