When the third Captain America film was in the early stages of development, Robert Downey Jr. and Marvel Studios were still embroiled in discussions for a new contract to see the actor return as Tony Stark. So with one-half of the “Civil War” conflict potentially unavailable, the Russo brothers had one old comic arc in mind to replace it.
Source: io9 – Before Civil War, the Third Captain America Movie Was Almost Based on This Wild Comic Book Story