To play a harder version of the boss in any area on all modes, you must have a shot down percentage of at least 98% (i.e., shot down 98% of the enemies/missiles) and cleared all ten layer levels in the area.

The boss will have a little more life, have a stronger version of at least one of its attacks, and will score more points in Score Attack and Direct Assault modes when defeated (e.g., the harder Area 1 Boss will give 20000 points when defeated as opposed to 10000 with the original).