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In 2014, after being exposed and defeated by Captain America and his allies in the Battle at the Triskelion, the high command of HYDRA ordered all of their sleeper agents to purge all S.H.I.E.L.D. loyalists or non-HYDRA agents and capture all S.H.I.E.L.D. facilities for assuring their survival.
Agents from the S.H.I.E.L.D. Academy were revealed to be undercover HYDRA operatives and attacked the Academy. Head of the Academy Anne Weaver was able to contact her former student Jemma Simmons and Antoine Triplett, who were stationed at the Hub and were currently unaware of the attack. Weaver used this time to warn Simmons and Triplett of the HYDRA threat before being cut off. 
HYDRA unleashed an enhanced individual to take the S.H.I.E.L.D. Academy. Weaver even managed to fight him toe to toe for a while, despite the fact that he was an eight feet tall man with skin as durable as steel. It took Weaver requiring seventeen bullets in the head to actually kill him. Despite that, she would have eventually lost to HYDRA if Agent Tomas Calderon had not arrived with a squadron of Quinjets to help save the Academy.
The saved students and agents were transported to the aircraft carrier Iliad, where HYDRA's moles were defeated through the efforts of Bobbi Morse, Isabelle Hartley, and Alphonso Mackenzie. The agents assembled on the ship eventually became the core of Robert Gonzales' S.H.I.E.L.D. faction.