"G.I. Joe: Retaliation" has a new trailer, which answers some questions as to how much of the story from the (unfairly-maligned, IMO) original film is actually being continued here. Answer: A whole bunch.
It also makes it clear that it will continue the first film's anti-private-military-contractor theme; with Cobra (formerly "M.A.R.S.") now emerging as a Blackwater-esque force brought in ostensibly to protect the U.S. from the (framed) "traitorous" Joes.