User blog comment:The Ironman/Confused/@comment-3406131-20131215121622/@comment-1458758-20131216064452

Marvel is split up into several continuities. For example, the Story in the Movies is One continuity, then the comics also have several, there's the normal continuity (Earth-616) then there's the Ultimate Continuity (Earth-1610).

In Earth-616, Peter's body has been overtaken by Doctor Octopus who is now acting as the New 'Superior' Spider Man

In Earth-1610, Peter was killed by a combination of the Punisher and a fight with several villains including the Green Goblin. In this continuity, after his death, Peter became known publicly as Spider Man and as a great hero. Miles Morales then took on the Mantle of Spider Man and is the New Spider Man as such.