Alternate missions can be accessed during the game depending on whether or not you succeeded in a mission's objective or not. The A-routes will give you the best ending possible while the B-routes will not.

Mission	How to unlock
Mission 3-A	Collect 300 coins in Mission 2.
Mission 3-B	Fail to collect 300 coins in Mission 2.
Mission 4-A	Capture 200 maidens in Mission 3-A or kill 100 mice in Mission 3-B
Mission 4-B	Don't defeat Corn Chiwa in Mission 1, don't collect 300 coins in Mission 2, and don't kill 100 mice in Mission 3-B.
Special Stage	Defeat Corn Chiwa, Collect 300 coins, 200 maidens, 50 showgirls, 300 more coins, and get to Takosuke before time runs out.