| > we saw the real Nick Fury, not an LMD. In Secret War?|
Secret War was when he went into hiding, and he was last seen in the final issue during the big fight. He quickly left the scene, and replaced himself with an LMD (which was then killed by Wolverine).
Since then, he has recruited his own superhero team, unofficially called the "Secret Warriors". They made their first appearance in the latest issue of Secret Invasion. We saw what he was doing between Secret War and Secret Invasion in the recent issues of Mighty Avengers. He was maintaining a low profile, found out about the skrulls, warned Maria Hill, kept in contact with a few superheroes (like Cap, Falcon, Bucky, etc), and recruited and trained his new team.