At the end of a stage, you’ll get score-affecting bonuses if you’re qualified for it.
Here are some of my bonuses:
Food Fetcher: Collect all 100% foods in the stage (don’t let any food to decay). Must collect at least 100 foods to get this bonus. [+75,000 Points]
Money Keeper: Same as Food Fetcher but coins [+75,000 Points]
Speed Runner: Clear the stage <2 mins(Tourist, Rookie) [+40,000 Points], <4 mins(Seasoned, Veteran) [+60,000 Points], <6 mins(Virtuoso, SSH) [+80,000 Points]. This can only achieve if the mission is >50% and the player must use no special weapons.
Perfection: Achieve all clear bonuses you can get in that stage and clear without dying, using any spec/satellites. [+100,000 Points]
Suggest more if you want