Agents of S.H.I.E.L.D. Season 5 has just rewritten the history of the Marvel Cinematic Universe. Recent episodes revealed that the last remnants of Hydra were working with an alien Confederacy, a group of races who had promised to save humanity from a terrifying threat. The latest episode, 'The One Who Will Save Us All', finally gave that threat a name; Thanos.
It's been a long time since Agents of S.H.I.E.L.D. had a direct tie-in to the movies like this. The last one was back in 2015, when Season 2 tied into the events of Avengers: Age of Ultron. Since then, the show has settled for thematic tie-ins; so, for example, when Doctor Strange added sorcery to the MCU, Agents of S.H.I.E.L.D. introduced the new Ghost Rider. Now, though, it turns out that every single event in Season 5 has really been building up to the day Thanos invades.
But here's the catch; this shocking revelation also transforms the history of the MCU. Because it reveals that, as far back as 2012, Hydra knew that Thanos was coming. This subtly rewrites every one of Hydra's acts in the MCU, from Project Insight in Captain America: The Winter Soldier to Daniel Whitehall's pursuit of Inhumans. This one little tie-in has subtly rewritten the history of the MCU.
Just How Much Did Hydra Know About Thanos?
In the aftermath of the Second World War, Hydra had reinvented itself as what Arnim Zola called "a beautiful parasite." Hydra agents infiltrated governments, companies, espionage agencies, and most notably S.H.I.E.L.D., working to guide humanity to a place where it would willingly surrender its freedom. But everything changed in the aftermath of the Battle of New York. Hydra moved swiftly to secure samples of alien technology; according to tie-in comics, Loki's Scepter was stolen the day after the Avengers triumphed. One such piece of alien technology was a communications and transport device, and Hydra managed to get it working. They got in touch with the Confederacy.
The Confederacy are a loose alliance of alien races and business cartels, including the Kree House Kasius. They've lasted over a thousand years, and excel at manipulating others. It didn't take the Confederacy long to realize that they were speaking with people from a world Thanos had targeted; it's even possible Hydra described Loki's Scepter, and the Confederacy recognized it as an Infinity Stone. They knew straight away that Thanos would return to Earth, and they used the threat of this return to begin to manipulate Hydra. They offered to save Earth if Hydra delivered its most precious resources - including "enhanced" beings. It's important to note that the Confederacy had no intention of honoring this agreement; they knew full well they couldn't actually stop Thanos. Instead, the Confederacy simply intended to plunder Earth before Thanos razed the planet.
Hydra is divided into "cells," and cell leaders don't tend to share information with one another. Agents of S.H.I.E.L.D. Season 2 revealed that some of these cell leaders are actually antagonistic towards one another, each pursuing their own agenda. So this knowledge likely didn't reach every Hydra cell leader we've seen since 2014. But it probably did reach key leaders who moved within the same circles as General Hale; that means it's reasonable to assume both Daniel Whitehall and Baron Von Strucker were part of this.
The Real Reason for Project Insight
Hydra, then, were the only ones who knew Thanos was coming. Hydra had played the long game for the last few decades, and it had paid off; but now time was running out, and they simply had to get the world ready to deal with an imminent alien invasion. The solution, to Hydra, was obvious; now was the time to rise up, to unify the world, and to begin preparing for Thanos's arrival. This new motive subtly explains why Hydra felt 2014 was the ideal time to step "out of the shadows, and into the light;" because they believed they simply didn't have any more time to wait.
Project Insight was born in the aftermath of the Battle of New York. Having had an up-close-and-personal look at a S.H.I.E.L.D. Helicarrier turbine, Tony Stark offered some improvements; and senior Hydra agents in S.H.I.E.L.D. saw the potential. They manipulated S.H.I.E.L.D. into launching a controversial program that would send three Helicarriers into the atmosphere - and, in reality, these Helicarriers would be programmed with an algorithm to target every potential threat to Hydra. Had Project Insight been a success, all resistance to Hydra would have been destroyed the moment it went live. Hydra would have literally taken over the world, uniting the planet under their authoritarian rule.
The key players in Project Insight were Alexander Pierce and Gideon Malick (who supported it as a member of the World Security Council). While Malick doesn't seem to have known about the threat of Thanos - he was more obsessed with the legends of Hive and Maveth - it's possible Pierce did. But Project Insight failed, and Pierce was killed by Nick Fury.