During the game, you will slowly earn fighting points. These fighting points are used towards unlocking secrets in the game. A total of 2000 points are required to unlock everything. Each level gives you about 50 to 100 points, ranging from the first to sixth level. The secrets are opened in the following order:

Extra lives: Extend up to 9 lives.
Stage select: Levels 1 through 6.
Color change for all characters: Also opens up Alpha Guy and Alpha Cody as two new characters. They look exactly like the ones in the Alpha series.
Rapid punch: Allows you to hold Attack to punch rapidly.