Scorpio and Zodiac used the Zodiac Key to reprogram the LMD and give it all of Nick Fury's memories. This LMD prototype was not a robot. It was a synthetic man. The prototype was designed to not have independent thoughts, but the Zodiac Key did something to grant the LMD prototype his own thoughts independent of the default artificial intelligence (AI) programming. After being caught by SHIELD at the fall of the Zodiac team, SHIELD scientists studied the LMD prototype to figure out how it could develop thoughts of its own. Even though the scientists (and Nick Fury) told it that it wasn't really Nick Fury, the LMD prototype kept blocking those thoughts and forgetting that he wasn't the real Nick Fury. Each time, the LMD prototype was told or shown that it wasn't Nick Fury, its mind would reset so that it would believe it was the real Nick Fury.