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#5 RIVALRIES WITH OTHER ORGANIZATIONS
In case you don't know, S.H.I.E.L.D. isn't the only acronym-that-spells-a-weapon secret organization in the Marvel universe. There's the European branch of S.H.I.E.L.D. called EuroM.I.N.D. Britain has their own version of S.H.I.E.L.D. called S.T.R.I.K.E. Another one, called A.R.M.O.R., we will probably never see because it's technically “so secret” that no one in the Marvel Universe knows it exists, plus their jurisdiction is anything that tries to break out of its own reality and come to another.
One more organization that stands a good chance of showing up is S.W.O.R.D. This particular acronym stands for “Sentient World Observation and Response Department.” They work closely with S.H.I.E.L.D. in the comic books, but they handle mostly extraterrestrial matters, and with the events of The Avengers and the upcoming Guardians of the Galaxy it seems logical that a few more aliens will be visiting Earth. Oh, and you know who created S.W.O.R.D.? Joss Whedon.
It's somewhat commonplace in these types of shows to have the occasional headbutting with similar organizations and usually it's with a group that has more power than the main characters, but it'll be pretty hard for someone to be above S.H.I.E.L.D. But if someone can take the secret organization that has the highest level of security and give it a humorous approach to its rivalry with another organization, it's Joss.