Re: "Mr. Stark, you've become part of a bigger universe."
Agreed... he seems fully briefed and on the "inside" of the operation. A role for Shield and Fury could be to inform Stark that they discovered a figure behind the Ten Rings group which is the Mandarin, and they want Stark to investigate... The story could go from there, and of course Stark does more than just observe.
Through-out the film there can be references to different associates of the Mandarin that are working to overthrow governments, etc... including a particular underground Neo-Nazi organization headed by an enigmatice character who was terribly disfigured with red face.