The default win condition for Free Enterprise is to defeat Zeromus, which requires the player to find a path to the moon to reach him, and to locate the Crystal used to unlock his final form. The various O flags are used to add additional/alternate objectives to the game progression.

When playing with objectives, an introductory sequence enumerating your objectives will play directly after the Enterprise launches. Objectives can also be viewed in the Track menu.

Free Enterprise technically supports up to 32 concurrent objectives, though it's not possible to reach that number with the current available flags.

Objectives may be completed in any order.