In Blinx 2 the player progresses through two intertwined campaigns as a member of both The Tom Tom Gang and The Time Sweepers. The goal of these campaigns is to acquire all eight fragments of "The Big Crystal" to prevent the end of the world. The Big Crystal, being shattered, had its pieces spread across time and space.
Once all eight Big Crystal pieces are collected your team of Time Sweepers are tasked with fighting a final Time Monster called The Scissor Demon. After the first stage of the fight the player's Tom Tom team will show up, uniting the Big Crystal which is then used to kill the Scissor Demon, ending the game.
As opposed to the first Blinx the player character is custom created by the player rather than being a unique character. Along with the player character the player is also responsible for assembling a team of fellow Time Sweepers/Tom Toms to use for special team stages. These team characters can be modified to the same degree as the player character after they are recruited.