The dissolution of S.H.I.E.L.D. in Captain America: The Winter Soldier will ultimately lead to the conflict at the core of Captain America: Civil War, according to a set report from Avengers: Age of Ultron.
Digital Spy has a list of 25 things they learned during their time on the set of the forthcoming Avengers sequel, and some of it comes from a pretty forthcoming conversation with producer Jeremy Latcham:
Much of the Avengers' problem boils down to their lack of a clear leader post-Winter Soldier. "SHIELD has fallen apart, so this movie becomes Tony Stark and Steve Rogers trying to put the Avengers together without a parental unit like Nick Fury hovering over them," explains Latcham. "What you realize is that these are guys who work best with rules, and probably do need some adult supervision."
And as anybody who watched the first film can guess, Tony and Cap aren't an ideal leadership pairing. "Tony has been paying for everything, designing stuff, building new toys, he's the benefactor of the whole thing. But Steve Rogers is very much in charge of operations and missions, he's the moral compass," Latcham goes on. "But how long can Tony Stark have someone else be in charge?" In other words, groundwork is being distinctly laid for the Stark vs Rogers core of Civil War.
In the comics, a conflict between a group of superheroes and a group of supervillains is ground zero for an explosion that kills hundreds, moving the government to pass a Superhuman Registration Act requiring anyone with powers to register with the government. Tony Stark and Steve Rogers end up leading opposing factions, with Stark supporting the act and Rogers opposing it.
The story ultimately resulted in Rogers' death (although he eventually got better), when he was assassinated by a brainwashed Sharon Carter (played in the films by Emily VanCamp) while in custody following the events of Civil War.