FTC complaints typically end in agreements--called consent decrees--between the FTC and business about how to change the businesses practices.
If the FTC and the business cannot reach a consent decree, the dispute goes before an administrative judge. The losing party can appeal--to the FTC. The business can file a case in federal court.
So The FTC is: prosecutor (in conducting investigations and filing complaints), the judge (when a matter ends with a consent decree), the appellate court (after appeals from an adminstrative judges ruling).