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Major spoilers for Captain Marvel can be found below. Do not proceed unless you've already seen it or really don't care.
From the moment that we saw that Samuel L. Jackson's Nick Fury would have both eyes in the 90s throwback film Captain Marvel, we all expected one thing, to learn how Nick Fury ended up sporting his trademark eyepatch. Well, that's exactly what happened, though it needs to be said that it certainly didn't happen the way we expected. It wasn't an injury sustained in an epic battle for survival, but rather a random event after all the danger had, seemingly, been survived.
Here's What Happened
The moment comes after Maria Rambeau has successfully evaded alien pursuers while Nick Fury sits in the co-pilot seat with Goose, the cat that stowed away on the ship. Fury is celebrating their success and also thanking Goose for the feline's assistance (more on that in a second), by holding the kitty vertically, with their heads at a level and Goose's front paws extended like arms. Goose apparently doesn't care for that, because the kitty reaches out and swipes at Fury's eye, an injury that appears to be minor at first, but in the film's final moments we realize that it was not. The eye is lost.
Of course, I sort of buried the lede up there (in an attempt to not put spoilers too early in this) because the fact is Goose the cat isn't really Goose the cat. He's actually Goose the flerken. Goose is an alien creature that looks like a cat on the outside, but is capable of extending multiple octopus like tentacles from its mouth that are able to do some serious damage. This ability is part of what lets Nick Fury and company escape the attacking Kree, but it also means that when Fury got scratched, it wasn't a simple cat scratch, it was alien creature scratch and who the hell knows what bacteria that thing was carrying?
Here's What Nick Fury Says Happened
While we know the truth, it seems that Nick Fury has decided to protect his ego and not reveal what actually happened to the people around him. At the end of the film Agent Coulson is speaking with Fury and he asks...
Is it true that the Kree burned your eye out?
Nick Fury has decided to keep Goose close but he's clearly not revealing to anybody else what the creature really is. Nick Fury has already begun to not trust anybody, giving us a glimpse of the man he will become in later (chronologically) installments of the MCU. It sounds like Fury may have started a rumor himself so that people thought they knew what happened. Fury doesn't technically lie, he tells Coulson he can neither confirm nor deny that story.
And let's face it, having your eye burned out by the Kree is a way cooler story to tell at SHIELD cocktail parties.
How Fury's Previous Comments Fit With Captain Marvel
On the whole, Nick Fury had remained quiet about his injured eye in previous films. He had only made one statement about what happened resulting in his loss of depth perception. In Captain America: The Winter Soldier Fury tells Cap that his lost eye came as a result of trusting the wrong person. Here's the exact moment below.
For what it's worth, the events of Captain Marvel could certainly be interpreted that way, that he trusted somebody and paid for it. Goose comes to Fury's rescue and really seems to be trying to help out our heroes. Fury thinks they're on the same side, and he trusts that the furry little flerkin isn't going to do anything that would hurt him. Turns out, that's not exactly the case.
Captain Marvel has some fun with the eventual reveal. Knowing that fans are waiting for this moment, Nick Fury actually injures the same eye in his first encounter with Captain Marvel and the Skrulls earlier in the film. It's a minor cut above the eye that he says is fine, but it's a bit of foreshadowing for what we all know will be coming at some point.
So that's how the Nick Fury became the one-eyed badass that we know and love today. It certainly wasn't what anybody was expecting, but it's something we clearly won't forget.