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In Free Enterprise, you are given the airship at the beginning of the game, and you may complete whatever quests are available to you in any order. Further, the Pass opens a passage in Toroia that will take you directly to Zeromus, whenever you are ready to defeat him.
Additional options allow for randomization of key items, characters, treasures, shops, and more.
There are some important gameplay changes from the original game to note; the NPCs in the training room cover the essentials, and a full detailed list of Free Enterprise's changes can be found here.