Time Machie ni Onegai differs from its predecessor by having its own unique gameplay modes rather than strictly following a TV game show format. The Time Machine mode involves traveling to different time periods and answering trivia questions in order to trigger famous events (e.g. Moses creating a path through the Red Sea for the Jews, the belligerents of the Three Kingdoms era attacking each other, apple falling on Sir Isaac Newton's head, etc.). The questions themselves, however, have usually nothing to do with the historical event in question.

Another mode in the game is called "Megaten Quest"; however, it is not a Megami Tensei related quiz, but rather an imitation of a first-person dungeon crawler with randomly appearing enemies who ask the player a certain number of question on various themes. The third mode follows the same quiz format with correctly answered questions leading to puzzle solutions, and is essentially the multiplayer portion of the game. In all modes, time limit is imposed on the entire round rather than on separate questions.