Master Score is the combined score from all stages (completed or not) within a given difficulty tier. Your Master Score defines your ranking on the global leaderboard for the Challenge Event. Stages can be replayed for the best possible score.
The score from each stage is defined by the enemies defeated, speed of completion and the amount of hero health left at the end of a stage. Big combos and great matches are also taken into account. Using Continues has a negative effect on the stage score.
Each difficulty tier in a Challenge Event has a separate Master Score, leaderboards and rewards. You can try to reach the top position on all difficulty tiers if you so choose.