There have been many speculations as to how Age of Ultron will go. After reading some info and doing some research, here is my theory.
(Given that this is also making some bold theories on what will happen in Captain America 2: Winter Soldier.)
Toward the end of Iron Man 3 we saw that Tony Stark was done with being Iron Man, giving that role up for Pepper Potts.
It has been confirmed by Kevin Feige that the Tesseract was the Infinity Stone of Space and the Aether was the Infinity Stone of Power.
My theory assumes that Loki's Staff housed the Mind Stone. It was shown the ability to be able to control people's minds (obviously). In The Avengers it was stated that it was powered by the Tesseract, however, that could be a simple mistake if they give off the same energy signature.
In CA2 Hydra will be involved, shedding some light on what SHIELD is doing behind the scenes. And there will be mention of the staff.
Skip ahead to Age of Ultron. SHIELD is still messing with the power of an Infinity Stone and it somehow comes in contact with the Iron Patriot suit, giving it sentience. As Ultron keeps himself in secrecy, waiting, watching how SHIELD treats those humans that they "protect", Ultron deems that they are not worthy of making such important decisions. Humans are illogical, emotional creatures incapable of making the cold decisions (ie Nick Fury canceling the strike on Manhattan)
As the movie rages on, and powers are shown off, it catches the attention of one Mad Titan. The cut scene at the end will allude to the fact that Thanos now has the Earth in site to collect the final Infinity Stone.
Let me know what you think. Anything to add? Any flaws