Triplicity is a race against time. As time continues to diminish you must collect gems and destroy balls to replenish the time. To destroy the balls you must get three balls of the same color to touch each other.
In Classic Mode the balls start out in a different world and you must bring them into another world before you can destroy them. You do this by shooting bullets at the ball. When a bullet touches a ball, the ball will be placed into the world where it can be destroyed.