its simple
you were captured and brainwashed to kill kennedy but resnov interfeared and reprobramed you to kill the 3 men who killed his frend and put him in vorkuda, so he breaks you out to go kill them but dies in the prossess, so all the times you see him after vorkuda, he isnt real its actualy you, so you kill the 3 guys but there is still the matter of dragovich he put you in vorkuda and is in posetion of the nova 6 and controlls the sleeper agents in america who are programed to release teh nova 6 in the USA, so you go to his under sea braodcasting station (where dragovich sending signals controlling the sleepers) so you kill him and blow up the station so every bad guy is dead, american is safe and kennedy is alive.......for a bit longer
get it?