Unlike Hydra's ancient progenitor in the MCU universe, Hive of Earth-616 was a product of modern technology. More precisely, it was the result of Hydra reverse-engineering Kree technology.
As early as WWII, Hydra had collected a vast amount of information on the Inhumans and Kree technology left behind on Earth. Through in-depth research, they came to understand the differences between latent Inhumans, ordinary humans, and mutants. Before awakening, Inhumans were no different from ordinary people, but once the Kree-altered genetic code in their genes took effect, they would transform into Inhumans and become powerful superhumans.
But they encountered a very serious problem: the catalyst needed to trigger it, the so-called Terrigen Mist mentioned in the records, simply could not be found anywhere on Earth.
It was not until more than a decade ago that Arnim Zola completed the research. By using another parasite studied by Hydra to replace the Terrigen Mist, they had the parasite devour a Hydra agent. Hive then gained his thoughts and consciousness, after which they used those parasites to infect humans capable of awakening as Inhumans.
This way, they could not only awaken superpowers but also be completely controlled by Hive. However, this method had two flaws. First, all the Inhumans were controlled by Hive like puppets, while Hydra had to maintain control over Hive at all times. Second, all the parasites would naturally coalesce into Hive, making the experiment impossible to replicate.
The reason this project had not been included in the Weapons Expansion Program was because its limitations were too severe. It had to be bound to Hive himself. But in return, so long as Hive remained a member of Hydra, they would possess an absolutely loyal bargain-bin Inhuman army.
Well, until now.
"Where the hell did Hydra get all these disgusting little bugs?