Iron Man 3

In this film we see War Machine’s armour coloured red, white, and blue which in the comics is known as the Iron Patriot though it is mostly worn by Norman Osborn and meant to symbolize and represent both Iron Man and Captain America. He decommissioned  S.H.I.E.L.D. and Tony Stark, ran his own government agency H.A.M.M.E.R., and became the leader of the Dark Avengers in which villains take the place of the true Avengers. 

The film is also inspired by the plot of the acclaimed Iron Man graphic novel Extremis, of which the title refers to an enhancer alternative to the Super Soldier program but with side effects such as mental instability, fire powers, and regenerative abilities. The mastermind is Aldrich Killian, a mere scientist in the comic who actually works for Maya Hansen, the actual developer of Extremis in the comics but role-reversed to be the scientist who provides the regenerative component of the enhancer.

Killian also mentions running a company called A.I.M which stands for Advanced Idea Mechanics, is a rival organization to Hydra, and is responsible for creating the intelligent android known as M.O.D.O.K. 

The only true way that this film connects to the MCU is the existence of Tony’s Iron Legion which acts as sentinel armours designed to serve and protect people which we see again in the next Avengers. Next is Thor: The Dark World where it immediately picks up after the events of the Battle of New York.