Unlike Puyo Pop Fever, which uses a simple menu, Puyo Puyo Fever 2 uses a map system to let the player navigate the game's menus. The map system is also reused in the nine courses to show the supposed path of the player's character. Several buildings are available around the map area, known as Primp Town, which was the setting of the previous game. These buildings include a tower for endless modes, a shop to buy items, a town hall to change options and save, a museum for viewing unlocked media and a playground for multiplayer games. You can also explore these areas and talk to the respective characters, where they may distribute items. Items can be used in each course. The game boasts nine courses, three times that of the previous title. The courses in the gamework in much the same fashion as those of the previous game, with the addition of the aforementioned map screen to show the player's route so far. Each part of the story involves a segment of dialog followed by a Puyo battle, with the exception of the ending sequence of each course. Gameplay mechanics remain mainly unchanged; however, the aforementioned items system allows the player to perform various different functions. Common items can be exchanged for points at Oshare Bones' shop. The game also includes a save system which is not used in any other game to date. It allows three concurrent save files, and lets players save at the beginning of any Puyo battle in story mode, so a player does not have to finish an entire course at once but can stop partway through.
Multiplayer
As in every Puyo Puyo game, this game allows multiplayer, and can support 2 to 8 players in the DS version of the game; other versions can only support up to 4 players. In this mode, players can play as any available character.
Endless modes
There are five endless modes in the game. Three of the endless modes were previously available in Puyo Pop Fever: Endless Fever, Endless Task, and Endless Original. Two new endless modes are also introduced: Endless Battle and Endless Chu Panic. The latter is the only mode in which Chu Puyo appear; Chu Puyo perform the same function as ordinary ojama puyo, in that they take up space in the player's dungeon and cannot be cleared unless normal puyo are cleared near them. Chu Puyo are heart-shaped and colored pink; chu is Japanese onomatopoeia for kissing.