In this mode, both players go at it head to head. In this mode, the player selects a character and battles against CPU opponents, leading to a climactic battle against Empress.

In the Super Famicom version, Fool (Easy) and World (Master) are introduced in this mode. Star (Expert) is only available in the Japanese version. When playing this puzzle mode longer, the game gets progressively harder, throwing in Ice Chunks, Bubbles, and giving the player less Crystals and Super Balloons. In this mode, the player either plays as Devil (Medium) or High Priestess (Hard) The goal is to survive as long as possible. The player is now given a much larger field spanning the entire screen, as well as a clown that can instantly teleport from the right edge of the field to the left and vice versa. The non-competition-based single player mode introduced in Magical Drop Plus 1! has been completely reimagined. The game also introduces Rainbow Balloons, colorless Balloons that will become Special Balloons when matched with two or more balloons of the same color. Special Balloons can now be matched with normal Balloons, unlike the first game where they must be matched separately.

The core gameplay is similar to that of the first game, though with a few additions and modifications.

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