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The Cube is a secret S.H.I.E.L.D. facility at a classified location.
HYDRA was forced to reveal their infiltration within S.H.I.E.L.D., and HYDRA operatives started sieging and attacking every S.H.I.E.L.D. facility they had access to, including the Triskelion, the Hub and the S.H.I.E.L.D. Academy.
The Cube was also attacked, and a HYDRA faction fought to control it. However, the HYDRA operatives inside were outnumbered by the loyal S.H.I.E.L.D. agents, and S.H.I.E.L.D. pressed the advantage, managing to retake the facility and maintain it as a secure facility. One of the HYDRA operatives inside, Kaminsky, escaped with a S.H.I.E.L.D. Helicopter and joined John Garrett at the Barbershop Headquarters in Cuba, explaining the whole situation.
- In the comics, the Cube was originally a S.H.I.E.L.D. black facility, one of nine classified bases and a prison for alien criminals who committed crimes on Earth.