The Avengers Set Up The MCU"s Next Civil War 11 Years Before It Happened

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Summary

The conflict between Iron Man and Captain America in Civil War was not the only one in the Marvel Cinematic Universe, and the second one was set up years earlier.
Nick Fury tried to prevent the second Civil War and the Skrull invasion from escalating to destructive levels.
Despite Fury's efforts, the Skrull invasion triggered a new conflict, with President Rison declaring all species not from Earth as enemy combatants, including Asgardians.

The conflict between Iron Man and Captain America won’t be the only Civil War conflict in the Marvel Cinematic Universe, and The Avengers set up the next Civil War a decade before it started. The MCU has seen a variety of conflicts between heroes, villains, aliens, and more throughout its five phases so far, and one of the most memorable ones happened in Captain America: Civil War. The Iron Man vs Captain America conflict marked a turning point in the MCU’s history, but it was only the first of its kind in this connected universe.
Although the tension between Tony Stark and Steve Rogers was evident since The Avengers, the Civil War battle was slowly built, and the same is happening with the second one. The events of the TV series Secret Invasion are now making way for a new, massive political conflict that is already escalating to destructive levels. Nick Fury (Samuel L. Jackson) was in the middle of it, and he also saw the development of the first Civil War, but he did his best to stop the second one a decade before it even started.
Nick Fury Prevented Secret Invasion's Ending War At The Start Of The Avengers

Nick Fury was aware of the problems that could arise once the Avengers were formed and started defending Earth in The Avengers, and he has done his best to prevent or stop many of them, risking his life in the process. Fury actually prevented the Civil War set up at the end of Secret Invasion in The Avengers, but the Skrull invasion ended up triggering this new conflict despite Fury’s efforts a decade earlier.
At different points in The Avengers, Nick Fury was shown talking to the World Security Council and trying to make them understand that the Avengers had everything under control, yet they still launched a nuclear missile to end the Chitauri invasion, not minding the destruction they would have caused. Among Fury’s efforts to make the Council rethink their plans and not target the Avengers was a conversation where the Council shared their concerns about Asgardians like Thor due to Loki’s actions. The Council was worried that Asgard was declaring war on planet Earth, so Fury clarified that Asgard wasn’t the problem – it was Loki, and Thor wasn’t a threat but was a potential, powerful ally.
Fury managed to divert the Council’s attention and they stopped seeing Asgardians as the threat, instead focusing on Loki and the Chitauri invasion. Unfortunately, this wasn’t the case in Secret Invasion, where, after the Skull’s presence and plans were discovered and they defended themselves, President Rison (Demort Mulroney) declared all species not from Earth to be enemy combatants, and that includes Asgardians.
How Nick Fury's Story In The Avengers Explains His Reaction In Secret Invasion

Ritson’s plans and reaction didn’t happen just because, and they were the direct result of the Skrulls' invasion and the attack on Ritson. In his statement, where he declared any species not from Earth to be enemy combatants, Ritson also declared that they would make sure to kill every last alien, for which Fury later scolded him. Ritson’s statement led to people killing those they suspected to be Skrulls, killing innocent people in the process, and Ritson’s plans would also include the Asgardians who are now living in New Asgard.
Fury was understandably aggrieved, but also not surprised as Asgardians had already been seen as a potential threat during the events of The Avengers. In the end, Fury was only able to delay the MCU’s new Civil War in The Avengers, but the events of Secret Invasion got out of hand, and not even Fury could have convinced the President to take a less aggressive approach.
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