Colonel Shaw calls Mystique into his office, over the connections between terrorist leader Nick Fury, when Wolverine was a part of shield, but Nick Fury has been dead for 20 years.
Flashback , Nick Fury has been arrested and is allowed to be free in exchange for him training new mutant recruits. One of the new recruits is Wolverine, who immediately gets promoted by Fury to squad leader. Fury is apparently killed by an explosion, wolverine was blamed for the explosion. Wolverine was stabbed in the head in a training exercise moments earlier and could not have been there as he was in the medical bay.