If you are using plugins like Pirate Guild or Yaki Armada which are using ADS to handle NPC ships, you will need to disable them first. It's usually done in your Artificial Life setting menu ( [Esc] / General / Artifical Life). After that:

1. Open the ADS Manager
2. Select Uninstall ADS
3. Save and quit your game
4. Go to your X3 Terran Conflict installation folder and double click the file called “Uninstall ADS.bat” (1)

(1) The default path is something like Program Files\Egosoft\3X Terran Conflict. It's different for Steam. But i'm sure you can find by yourself with the help of a mighty search engine.