Whitehall was killed before he could fully exploit the Obelisk, his second in command Sunil Bakshi was captured, and many other heads of HYDRA were killed by HYDRA itself when S. Hydra personnel are issued cowled jumpsuits, which have included a number of designs over the years. When Coulson learned that the name of the project was Project Destroyer of Worlds, he was suddenly horrified and claimed that S. However, that scene contradicts the events of Captain America: First Vengeance where HYDRA still works for the Nazis after the imprisonment of the Howling Commandos.

In 1970, after Wilfred Malick―a head of HYDRA―passed away, his sons Gideon and Nathaniel Malick visited Werner Reinhardt in the Rat. When it became clear that Rogers was gaining the upper hand in the fight, the Red Skull attempted to use the power of the Tesseract with his bare hands. Spider-Woman refused their offer, destroying in an explosion the Hydra base to which she had been taken. Keeping true to its oath, HYDRA would continue to operate following the death of Hale and the collapse of her HYDRA cell, though they were scattered and a husk of its former self.

Meanwhile, Gideon Malick and Hive had a dinner, in which the latter was able to tell that Malick was after true power. His ersatz coup d'état paid off, and Hardball is appointed as the new Supreme Leader of the organization, severing every tie with his former life. Ruby tricked her mother and locked her in her own room so she and Strucker could go to the HYDRA Herefordshire Facility. Using the HYDRA data, leaked by Black Widow, Helmut Zemo hunted down and executed multiple HYDRA members who worked on the Winter Soldier Program to prevent the super soldier production from restarting.

As men brought in Hinton, Hive told Malick it was time to reveal themselves, setting Phil Coulson's Prosthetic Hand on the table and informing Malick that he planned to take over Transia Corporation to achieve his desire. When Hydra scientists were recruited by America as part of their efforts to use their weapons genius, they were able to subtly subvert S. Convinced that other leaders of HYDRA wanted to eliminate them, he and Bloom contacted Doctor List, who assured them that he and Baron von Strucker were not involved in any attacks on them.The battle left the Triskelion in shambles and resulted in the deaths of many HYDRA agents, including Pierce.

Malick's men had their guns personalized so that only a person with the correct fingerprint could use them. The agents were successful, but they were soon discovered and chased by Rogers who managed to capture all of them. It was founded in ancient times, formerly as a cult dedicated to the fanatical worship of Hive, a powerful Inhuman that was exiled to the planet Maveth by ancient Inhumans. However, even their experiments came to an end when the Avengers attacked Strucker's fortress in Sokovia, killing List and capturing Baron von Strucker, who was later killed by the robot Ultron.As Creel came to Phil Coulson's room to confront him, Coulson convinced him to escape the HYDRA Preparatory Academy with Glenn Talbot.