Overlord Laharl has decided to cut the Prinnies' salaries after he has been "assassinated". As a Prinny who found a magic watch, the player has to go back in time to find out what has really happened. To do so, Prinny can possess various characters from the Disgaea series and follow them through the plot. In order to change the past, he can also Mind Control the character he is possessing when said character has to make a choice. Mind control allows Prinny to select one of three options that will change the series of events from that point. At a few points in the game, when major events occur or are prevented from occurring, Prinny's soul is "saved", meaning that the next time travel will send him back to that specific point to start over. The goal of the game is to start over and over, finding as much information as possible and prevent Laharl from being "assassinated" and saving the future of the Prinnies' salaries.
The story is presented in the form of dialogues between the characters, as well as sprite animations. And has many different endings, depending of the choices made by the player. The endings are themselves often short advertisings for Disgaea and Nippon Ichi Software games.
To follow the story's progress, the player has access to a time table of all the events, following every character's steps, Prinny's diary, giving clues about the plot and how to change how the story unfolds, and a database of the characters, places and other trivia from the Disgaea series, and sometimes for other Nippon Ichi Software games.