The main character (a boy whose default name is Yumil, or a girl whose default name is Tia) has been having nightmares about the end of the world. They are told that they have been chosen by the powers-that-be - but not to save the world. Their job is to use a magic tome called the Book of Prophecy to record what is worth saving, so that that information may be used to create the next world.
The protagonist finds and befriends four helpful Spirits taking residence inside the Book. Throughout the journey, they learn about a plot to hasten the end of the world, as well as what happened to the Book's last Chosen One.
The plot, as well as the gameplay, revolves around the Book of Prophecy and the touch-sensitive lower screen of the DS. To record a person, monster, plant or weapon in its pages, the player performs a "Code Scan", which is done by hitting the target to be scanned with the Book itself. Each page shows the object's basic information, such as attack strength (for items), health points (for enemies) and personal likes, dislikes, and goals (for people).
In addition, everything that can be scanned has a Code - which is like DNA, but simpler. Its Code is in turn made up of many Codes, which are pieces of different shapes and sizes that fit into the object's grid somewhat like fitting pentominoes into a box. Creating different combinations of Codes, by adding and removing them, changes the object's title and sometimes has a major effect on the object. Changing titles to remove 'defective' Codes, as well as creating 'new' items, is a facet of gameplay used in many sidequests and occasionally within the story.