Captain America: The Winter Soldier revealed that the terrorist organization Hydra had infiltrated SHIELD and had been slowly building power to take over SHIELD. As the organization is in shambles of its former glory, their role in the new Avengers movie could be limited. This creates some issues for the Avengers. SHIELD put together the Avenger initiative to deal with threats that were too powerful for the agency to handle on its own. The Avengers would be summoned as a last resort to combat these kinds of massive threats.
No More SHIELD Leadership
SHIELD may no longer be the leading organization for the Avengers. There is a bit of foreshadowing at the end of the Avengers movie that they may be getting their own base of operations in New York City. Stark Tower had taken some serious damage during the battle with the alien army and Loki. The most noticeable aspect of the damage was the Stark sign on top of the building. Only the A was left in the Stark name and it could mean that Stark Tower will now become the Avengers base. In the comic version, Tony Stark helped to fund the Avengers and gave them the use of his New York Mansion as a base. The mansion came with a full staff which included a butler named Jarvis.
No Appearance by Director Coulson
The Avengers believe that Agent Phil Coulson died in the last movie. None of them are aware that he is alive and none will be aware that he is the new director of SHIELD. The director of Age of Ultron has already stated that there will not be a reunion with Coulson in the movie. This may also mean that there will be a limited role for SHIELD in the movie.
SHIELD will be represented by other agents
At the end of Captain America: The Winter Soldier, the various agents of SHIELD went their separate ways taking employment elsewhere. Some of the main characters have recognizable positions. Maria Hill was seen working at Stark Industries. Nick Fury is assumed dead but will make an appearance in the film. However, the Black Widow and Hawkeye will both be in the film but their role with SHIELD may be limited.
Shaping the new SHIELD
Nick Fury named Phil Coulson the new director of SHIELD and gave him the task of rebuilding the organization. How this takes place and what Coulson does to bring the organization back together will fit into the Avengers movie in some way. Whatever direction the series Marvel’s Agents of SHIELD takes will also play a factor in the new movie.