^ Pretty much got it. Otto blocked Peter's hack of the octobot...but Peter might have been able to use it to transfer his conscience into Otto's brain. There is a panel in Avenging where Otto reacts to a mugging despite himself, and dismisses his reaction as nothing but instinct. The word instinct is in bold.
Peter is not dead, Bruce Wayne didn't die either, he was sent through time, and nor did Johnny (he was merely trapped in the Negative Zone and thought dead by Ben).