It starts off seeing The Destroyer after Thor. It is taken away by Phil Coulson and S.H.I.E.L.D., and a year later (around the time Steve Rogers is found), Coulson checks in with the research team to find that they can actually control the Destroyer. The level of control they have isnt specified, whether they can just turn it on or actually choose its targets. Coulson tells the scientist he wants them to "Dismantle the thing and make it about a hundred times smaller...And put a trigger on it!"