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Official Square Enix Policy
Third party tools are cheating tools that give an unfair advantage. All of them are completely banned both in Final Fantasy XI and Final Fantasy XIV. Violators of the ban may have their access to the game suspended or revoked. The GMs investigate reports of third party tool usage and punish the players responsible. Players who download third party tools are placing their characters and account at risk from both official punishment and malware-containing programs.
Unofficial Square Enix Policy
In actual practice, Square Enix is notably more lenient towards third party tool users than their official policy suggests.
Square Enix's unofficial policy towards third party tools has been described as "see no evil, hear no evil, speak no evil":
Square Enix takes no effort whatsoever to actively look for most third party tool users, with the exception being anti-RMT campaigns. Contrast with World of Warcraft's "Warden" program, which actively scans players' computers looking for cheating tools and other unauthorized mods.
When determining whether a user under investigation is using a third party tool, absolutely no evidence outside the game is allowed into consideration. It does not matter how many screenshots or forum posts the player shows or admits their guilt in. Only a confession in-game is valid. Contrast Square Enix's own policy for banning RMT players, who may be banned merely for a suspicious pattern of behavior with no hard evidence of any kind. Hence, what is known as the "Fight Club" rule ("The first rule of Fight Club, is you don't talk about Fight Club"): never talk about the third party tools you use in-game.
Square Enix almost never makes any effort whatsoever to alter their client to either introduce incompatibilities with known third party tools or alter the client behavior that allows the tools to function. For example, there is a third party tool that allows players to see a fellow party member's TP; normally, a player sees only their own TP. But the server sends data to the client telling it what every party member's current TP is, and it stores this data in memory even though it has no authorized use. The tool merely needs to read those memory locations to gain the information.
Square Enix will delete any posts made on their official forum that mention the names of specific third party tools, and the poster will be punished. This impedes attempts to bring known issues with third party tools to Square Enix's attention. Many players have received the impression that they have no intention of doing anything about third party tools and would just rather not hear about it.