It's a Trap!
Sharon Carter ran into the base with a dozen S.H.I.E.L.D. agents at her back. Intel had said that HYDRA was working on a new weapon at this location and Sharon led a team in to recover the weapon and the data on it. They stormed in with guns blazing.

Sharon had gotten into the main computer room and started downloading files when there was a sharp prick to the back of her neck.

Then the world went black.