MCU Film Theory: Nick Fury Has Been An Alien ALL ALONG
Looking at the Fury who turns up in Iron Man for the first time and the one we get to know more in The Avengers with greater depth, he's markedly different to the one we met in Captain Marvel. Sure, he went through some stuff and he lost the use of an eye, but the two could be entirely different people. Even with the assumption that time changes all men, it's a bit of a leap, particularly when there was apparently nothing catastrophic enough in that time to warrant speeding up the assembly of his dream team.
So is the Fury who turns up to recruit Tony Stark really Fury? There are signs that it's not. The first hint that Fury is not himself in Far From Home, in hindsight, comes when he acts in a way that is not befitting what we'd expect of him. As Talos later clarifies, he's "not very good" at standing in for Fury, despite knowing him intimately thanks to the Skrull ability to absorb experiences and memories. That's presumably why he doesn't have the judgement skills to realise Mysterio is a charlatan.
Maybe that's why Fury attempted to recruit Stark as the founding stone of his Avengers despite him failing Black Widow's assessment of him and being uninvited from the Initiative pretty quickly afterwards? That doesn't sound like the smart judgement of the real Fury does it? Sadly for him - and the writers - that has to have been Fury, because of what comes next.
He next turns up in Iron Man 2 briefly and in the Thor post-credits, asking Professor Selvig to work out what the Tesseract was and its powers, confirming that while the Security Council had asked him to investigate it rather than searching for Captain America in the period between 1995 and 2008, he had made largely no strides. Almost as if he was pre-occupied. But more importantly, him asking for Selvig's help means he wasn't in touch with the Skrull at this point, because they were aware of what the Tesseract was and the potential it possessed.
But what if this point was a trigger for Fury to seek more answers of his own from the only other source of knowledge on the Tesseract he could find? After all, Fury's Initiative was given an almighty shot in the arm during the events of Thor by the "invasion" of the God Of Thunder and the Destroyer in New Mexico. He knew, at that point, that SHIELD defending against Earth-bound threats wasn't enough - he needed a means to defend against the alien threats that had been announced to the Earth.