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In Thor when S.H.I.E.L.D "appropriates" Jane's stuff, when she asks who they are Erik says

I knew this scientist, a pioneer in gamma radiation. S.H.I.E.L.D showed up, and that's the last I heard from him.

I assume he is talking about Bruce Banner since S.H.I.E.L.D had a file on him for the Avengers Initiative and he was working on gamma radiation for regeneration (according to the 2003 and 2008 films).

Erik seems to imply that S.H.I.E.L.D had a hand in Bruce's disappearance and they knew where to find him in The Avengers (though that could just be Intel gathering).

So i am wondering, what was S.H.I.E.L.D's role in Bruce Banner's Origin story in the Marvel Cinematic Universe?

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    I think the implication is that they turned up and took his stuff away – Valorum Nov 19 '17 at 9:09
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    ...and covered up what happened...which would be S.H.I.E.L.D.'s standard operating procedure. Recall the cabin built to hold Banner? At some point he seems to have been there...judging by the fist shaped dent in the wall. – Paulie_D Nov 19 '17 at 12:04
  • It might even be said that the reason that S.H.I.E.L.D started to "appropriate" stuff was because they were too late to stop Banner from trying to recreate the Roger's experiment. – Odin1806 Nov 24 '17 at 21:49

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