Agents of SHIELD season 7 could reveal the real history of Hydra. The final season of Marvel's Agents of SHIELD is expected to be its most spectacular to date, with Mack and the SHIELD team using time travel to explore the history of the Marvel Cinematic Universe.
SHIELD appear to be caught in something of a "Time War" with an alien race known as the Chronicoms. The Chronicoms are invading Earth in the present day, and they believe only SHIELD can stand in their way. As a result, they're using time travel to rewrite the past and ensure SHIELD aren't a threat. Meanwhile, Fitz and Simmons have cracked time travel as well, and they've sent at least one team - probably more - into the past to counter the Chronicoms. It's reasonable to assume they have a plan, not least because Fitz and Simmons have clearly learned how to slow down time, which means they could have been working on this for years.
The Time War plan is expected to explore several periods of SHIELD's history. Agents of SHIELD season 6's finale saw Mack and his team transported to the 1930s, before SHIELD became the SSR. There have been rumors that Hayley Atwell may have been on set as Agent Carter; Patrick Warburton is returning as Rick Stoner, the SHIELD agent who built the Lighthouse in 1970; and the first Agents of SHIELD season 7 trailer teased Hydra, presumably to be encountered in the past. All this means a number of time periods are set to be explored. Just how do Fitz and Simmons think they can stop an alien invasion through time travel?
How The Chronicoms Know SHIELD's History
In order to work out how to beat the Chronicoms, you logically have to begin with an assessment of their capabilities. There are probably more time traveling Chronicoms than SHIELD teams, and they're attempting to rewrite history to ensure the present-day SHIELD is weaker. They're helped by centuries of anthropological research conducted by Enoch, and by Nick Fury's Black Box. The Black Box was a portable Vibranium hard drive created by Fury, containing everything he believed a SHIELD director needed to know - including all the darkest secrets of SHIELD's history.
The Chronicoms successfully acquired the Black Box in their initial strike at the Lighthouse in the Agents of SHIELD season 6 finale. That means they know everything Nick Fury himself ever knew about SHIELD. They can position themselves carefully to change the past, introducing weaknesses in SHIELD technology, diverting resources to prevent strategic assets being created, and perhaps even replacing key operatives with Chronicom doubles. The trailer showed them traveling back in time and using face-stealing technology, which means it wouldn't be hard for them to infiltrate SHIELD in the past and sabotage the agency from within.
Nick Fury Didn't Know Everything About SHIELD
Fury's Black Box may be a tremendous repository of information, and crucial to the Chronicoms' plans, but it may not give them quite so sizable an advantage as they believe. The simple fact is that Nick Fury didn't know everything about SHIELD. He was unaware of Hydra's infiltration until Captain America: The Winter Soldier, and Agents of SHIELD season 5 included flashbacks that revealed the sheer scale of the Hydra operation. By the 1990s, Hydra had successfully constructed their own dedicated installations, including a Hydra Academy, all of which were naturally kept off SHIELD's official records.
Meanwhile, Agents of SHIELD season 5 also confirmed that there were other secrets woven into the history of SHIELD. The Lighthouse itself - a base literally designed to survive the end of the world - had been constructed by SHIELD in 1970, and all official records had been scrubbed. Coulson found no hint of the Lighthouse's existence in Fury's Black Box, which suggests this was another thing Fury didn't know about. All this means there are limits to the Chronicoms' knowledge; they don't know much about Hydra's secret operations inside SHIELD, and projects as significant as the Lighthouse aren't recorded in the Black Box either.
SHIELD Need Hydra To Defeat The Chronicoms
The Chronicoms aim to rewrite history to ensure SHIELD isn't a threat in the present day; SHIELD's best tactic would be to take a similar approach, subtly adjusting the past so they have a better chance of repelling the invaders in the present. Ironically, the historic Hydra infiltration means they have an easy way of ensuring they have resources and weapons the Chronicoms don't know about. They could use Hydra to create these in the past, ensure all records are erased so they're not contained in Fury's Black Box, and then use them in the present day.
It's important to remember that, with a handful of exceptions, high-level Hydra leadership had the tendency to run down family lines such as the Sitwells, the Von Struckers, and the Hales. That means SHIELD can quite easily identify key Hydra leaders in any given generation, and can safely assume many of their closest compatriots were also Hydra. A few days of careful observation with present-day tech would probably remove any doubt. That means SHIELD know exactly which groups they can manipulate. Even better, when Hydra have served their purpose, SHIELD have had Project TAHITI-based memory-altering technology since season 1. They can literally erase all memory of their actions, ensuring Hydra never used the resources they've created.
Could SHIELD Create The Modern Version of Hydra?
Conveniently, if Hydra didn't exist, then Mack and his team would have a harder job. That raises an intriguing question. Whether or not Fitz and Simmons adjusted the past, secretly orchestrating Hydra's infiltration of SHIELD in order to create a resource they could use as part of their Time War. The Agents of SHIELD season 6 finale confirmed that Simmons is crossing ethical lines she'd never have considered before - she'd previously have found the idea of a Coulson LMD to be horrific - and she hinted that they're using other unsavory tactics.
All this would mean that Fitz and Simmons have created a time loop, where the past and the present feed into one another, a similar phenomenon to the one they encountered in Agents of SHIELD season 5. There's a sense in which they could be the ones who have created the modern incarnation of Hydra, the group who had successfully infiltrated SHIELD, in the knowledge that they are a necessary evil to ultimately save the planet. It's a chilling concept, and it would bring Marvel's Agents of SHIELD full circle, a fitting end to Marvel Television's flagship TV series.