Project Mr. Blue is S.H.I.E.L.D.'s name for their research on Samuel Sterns' mind after being mutated by the blood of Bruce Banner.
Agent Natasha Romanoff discovered an insane Samuel Sterns in the rubble of his apartment after his encounter with Emil Blonsky. She shot him in the leg and captured him after he tried to convince her to work for him.
Sterns was being held at a secure location and being studied by S.H.I.E.L.D. scientists.