Player vs Computer mode, A kind of story mode, shows the origin game of each character. Puzzle mode, It consists of a branch of levels, where the player advances choosing between 2 possible paths until reaching the end, in a total of 30 levels. In the Nintendo 64 version, a 4-player simultaneous option is available. As in Bubble Bobble, the 1st player, when he/she picks Bub, gets Bub, and the 2nd player gets Bob. The ability to choose a character was introduced. This game also marks the introduction of new bubbles: Rainbow Bubble (when bursting the bubble next to the rainbow bubble, the rainbow bubble will assume burst bubble color), Star Bubble (hit it, the star will burst all of the same colored bubbles on the screen), Metal Bubble (all bubbles in the path of the metal bubble will burst), and Trouble Bubble (this bubble cannot burst). Each scrolling playfield occupies the same space on the world map as five previous levels. Gameplay is further varied by the implementation of new scrolling playfields that are several times as high as the screen and must be conquered as an endurance event. Despite this some versions include a reimplementation of the Puzzle Bobble 2 levels now built around nodes (entitled Version 2.5). The player is not penalised if such bubbles again leave the playing field without attaching to anything (except for adding to the number of moves until the field is pushed down by one empty line). One result of this change that may appear strange to players of previous versions is that shooting a bubble to the top of the visible playfield without striking any bubbles causes it to bounce and start travelling back downwards.

When a node is no longer connected to any bubbles, it will disappear and when all nodes in a level have vanished the level is complete. The game completely abandons the idea of previous titles that the playfield is being pushed down by some sort of mechanical device and instead attaches groups of bubbles to nodes that move downwards.

Bubble bobble n64