Ultimate Spider-Man #17: Clone Saga
by Brian Michael Bendis & others
This volume answered the questions I had about a particular character. It also changed EVERYTHING in poor Peter Parker's reality. People seem to come back from the dead, including his father. Clones are made of Peter and experimented on so there are weird variants (Scorpian!Peter, adult!Peter, female!Peter) and not all the clones are completely mentally or physically stable. This is a big problem, as one might guess. The bigger problem is that it's impossible to hide this from the city, S.H.I.E.L.D. and Fury, the Fantastic Four, MJ, Kitty, or Aunt May. Everything gets turned on its head and Peter is left alone in the middle, just trying to hold on to reality.
This was beautifully and powerfully written. It's definitely a huge turning point in the series, and it was done really well, though it was very dark and difficult to get through at times because things kept getting worse and worse with no solution in sight.