4. Nick Fury Vs S.H.I.E.L.D./Secret Invasion
In the Nick Fury vs S.H.I.E.L.D. comic S.H.I.E.L.D. gets taken over by a group of pissed off Life Model Decoys (in the comics S.H.I.E.L.D. has the capability of creating near perfect clones of anyone) calling themselves Deltites and Fury has to battle his own spy group before he gets captured and replaced by an LMD himself. The Secret Invasion was a massive crossover that had The Skrulls infiltrate world governments and super-hero teams in a bid to take over the planet. Being an LMD is the primary theory floating around about how Agent Coulson is alive after being shanked by Loki in the Avengers movie. I don't subscribe to that theory just because the introduction of LMD's completely removes any stakes in this show and the Marvel cinematic universe as a whole. After all, if you can just bring back an identical copy of anyone who dies then what is the point of caring about these characters well-being in dangerous situations? So count me in as being totally anti-LMD. This brings me to my little idea of merging the Nick Fury vs. S.H.I.E.L.D. and Secret Invasion storylines with Skrulls (or Dire Wraiths if the Skrulls are licensed out to another studio along with the Fantastic Four) taking the place of LMDs. We would get a full scale alien invasion but done in a very clandestine way that works within the confines of a TV show budget and covers the inevitable question of why the Avengers aren't involved in the storyline. This would also be a good way to bring S.W.O.R.D. into the show too.