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Warning: SPOILERS for Marvel"s Agents of S.H.I.E.L.D. season 6
Marvel"s Agents of S.H.I.E.L.D. just surprisingly eliminated a major villain from season 5 - the Confederacy - and it happened off-screen! In Agents of S.H.I.E.L.D. season 6, the super spy agency is split between an Earthbound squad led by S.H.I.E.L.D."s new Director Alphonso "Mack" Mackenzie and Daisy Johnson"s team in outer space. S.H.I.E.L.D."s intergalactic mission is to find Leopold Fitz and reunite him with his wife Jemma Simmons. Naturally, Quake"s Agents are running into assorted aliens and enemies in the final frontier, but the reveal that the Confederacy is no more is a big surprise.
The Confederacy was a thousand-year-old intergalactic alliance comprised of six races: the Kree, the Kallusians, the Astrans, the Remorath, the Rajaks, and an unknown sixth species. In Agents of S.H.I.E.L.D. season 5, the Confederacy was unveiled as a threat to Earth that had been lurking in the background of the MCU since The Avengers. After the battle of New York in 2012, Hydra used a recovered Chitauri transceiver to strike a deal with the Confederacy: in exchange for their protection from Thanos, Hydra"s General Hale would provide the Confederacy with Gravitonium and Inhumans. However, General Glenn Talbot infused himself with Gravitonium and gained a leadership position over the Confederacy. Ultimately, when S.H.I.E.L.D. defeated Talbot and foiled the Confederacy"s invasion of Earth, the aliens never obtained the Inhumans and Gravitonium they desired.
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Since then, Agents of S.H.I.E.L.D. season 6 has introduced new alien villains: the Chronicoms, who are a race of ancient synthetic beings. Enoch, who set Agents of S.H.I.E.L.D. season 5"s time travel plot into motion so the heroes could save Earth from destruction, is a Chronicom anthropologist. But there are other kinds of Chronicoms, including Hunters, who are the most dangerous members of their race. Indeed, it turns out the Chronicoms are the ones who put an end to the Confederacy.
In this week"s episode, "The Other Thing," S.H.I.E.L.D."s ship, the Zephyr-One, was ambushed by Confederacy starships. However, the Agents soon learned that the Chronicoms had taken over the entire Confederacy fleet and wiped out the alien alliance. As the Chronicom named Atarah explained, their homeworld Chronyca-2 was destroyed by a mysterious plague. The Confederacy came to Chronyca-2 to "pick the planet"s bones clean" but the Chronicoms fought back with the goal of taking over their warships. While the details are scarce, the end result was that the Chronicoms defeated the Confederacy, and they now control the alliance"s fleet of ships.
This means that the combined aliens that threatened Earth in Agents of S.H.I.E.L.D. season 5 were wiped out off-screen; however, it also likely means that the Chronicoms only eliminated the aliens who were aboard the Confederacy ships and not the entire races themselves. After all, the Kree are part of the Confederacy and they are still a vital part of the MCU thanks to Captain Marvel and Guardians of the Galaxy and it"s highly unlikely Agents of S.H.I.E.L.D. would be allowed to close the book on the Kree in the MCU. Interestingly, in the Agents of S.H.I.E.L.D. season 6 premiere, "Missing Pieces", the Zephyr-One narrowly escaped from a Confederacy ship - but if the Confederacy fell before this encounter, that means the Chronicoms were in control of that ship but S.H.I.E.L.D. (and Enoch, who was traveling with Fitz to the planet Kitson) had no idea.
Meanwhile, the story Atarah told of how the Chronicom homeworld was destroyed could be linked to the mysterious alien parasites called the Shrike that have begun to infest Earth, and it"s possible Chronyca-2 was also a victim of the Shrike. Since destroying the Shrike is the reason Sarge, Phil Coulson"s doppelganger, has come to Earth, the two storylines of Agents of S.H.I.E.L.D.
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season 6 could be more interconnected than it first appeared. But with such deadly new villains to contend with, the silver lining is the Confederacy is now one less problem S.H.I.E.L.D. has to worry about, thanks to the Chronicoms.