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The day Tony Stark returns from Afghanistan, he holds a press conference. You can see Agent Coulson in the crowd.
I think no-one knows that Tony will become "Iron Man" at that time.
My question is when did S.H.I.E.L.D start to keep an eye on him?
Until that press meeting, Tony was just a businessman who created new weapons.
Was S.H.I.E.L.D following him for his weapons?
It is likely Tony Stark has always been under the watchful eye of SHIELD.
Given that his father held a Top Secret clearance and was one of their most well-known, well-respected and prolific scientific minds, like his father, they would have likely kept Tony under observation for any indications of similar intellectual propensities.
It is unlikely Tony would have been able to hide his intellectual prowess from his school administrators (he was too vain and arrogant to hide his abilities). If anything he would be closely watched for any indications of genius, for selfish reasons of course; successful alumni are an asset to a university. SHIELD would be sure to be monitoring that same information for almost the same reasons.
Even if Tony had not turned out to be the extraordinary genius his father was, he would eventually inherit the Stark Industries business, one of their primary weapon providers, and they would have kept an eye on the company for its technological developments, if for no other reason.
Yes, in the comics, Howard Stark helped create S.H.I.E.L.D., and even if they didn't keep that in the movies, Stark Industries is still an advanced weapons manufacturer.
So, SHIELD would always be keeping a close watch on Tony (because he's a genius and the son of Howard Stark) and his company (for the advanced tech and weapons).
