Why Nick Fury was not in Captain America: Civil War is a question that has followed the MCU since 2016, but it can be answered by both story reasons and behind-the-scene reasons. While Captain America 3 could have been a Steve Rogers story only, Marvel ended up signing Robert Downey Jr. for a role in the film that would become an Avengers-level event. The comic book arc Civil War was taken as an inspiration for the movie, and pretty much every Avenger in the MCU was brought for the movie – not to mention the MCU debuts of Black Panther and Spider-Man.
The scale of Captain America: Civil War could not be compared to any other previous solo MCU movies. The story took place in many different places, countries, and governments from all over the world wanted the Avengers to respond to their acts by signing the Sokovia Accords, and even the reclusive Wakanda stepped into the discussions. With so much at stake for the Avengers and for the rest of the world, it made sense for Civil War to involve so many characters, and the only absences that could be easily explained were that of Thor and Hulk, who were both off-planet.
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For that reason, it was hard not to notice Nick Fury’s absence in Civil War. Fury had been the mind behind the Avengers initiative, and even after the team became steered away from SHIELD, the Samuel L. Jackson character continued as a trustable friend of Stark, Rogers, Romanoff, and the others. Civil War happened two years after Captain America: The Winter Soldier in the MCU timeline, meaning that SHIELD was no more by the time the conflict between Iron Man and Captain America happened. Even still, Avengers: Age of Ultron’s helicarrier
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