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In The Avengers Fury explains that the reason why S.H.I.E.L.D was making weapons with the Tesseract was because of Thor's fight with The Destroyer and the sudden realization that there were aliens and that Earth was hopelessly outmatched.

Bruce: I'd like to know why SHIELD is using the Tesseract to build weapons of mass destruction.
Fury: Because of him. (pointing at Thor)
Thor: (STUNNED) Me?
Fury: Last year earth had a visitor from another planet who had a grudge match that leveled a small town. We learned that not only are we not alone, but we are hopelessly, hilariously, outgunned.

Source: IMSDb - The Avengers

However in Captain Marvel, which takes place before Thor, Fury met aliens and saw what they could do where Ronan was about to bombard Earth from orbit and was shot at by 2 Kree ships.

Now while we know that production wise Thor was the first film showing Earth's "interaction" with a species from another world but chronologically wise it's not. So is there a lore based reason why Fury blames Thor for showing how outmatched earth was to the rest of the universe?

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    recent events are more difficult to forget? – Zaid Syed M Md Mar 9 at 7:51
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    Fury is not blaming Thor specifically - he is using Thor as an example, since he's standing right there. – HorusKol Mar 9 at 14:20
  • Rule one: Fury lies. – Paul D. Waite Mar 18 at 14:55
  • @PaulD.Waite i thought that was The Doctor's rule – Memor-X Mar 18 at 21:42
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    @Memor-X: Fury says he had it before the Doctor. The Doctor says he had it before Fury. Which is true? (Show your working.) – Paul D. Waite Mar 18 at 22:09
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The damage done to the Earth in Captain Marvel is literally nothing compared to destruction due to the fight between Thor and the Destroyer. Besides this, Captain Marvel takes places years before Thor and only a few people know about her.

The damage done to the Earth during Thor was witnessed by many people and was the most recent one. So, he is just taking this one as an example why he had to use the Tessaract to create the weapon capable of mass-destruction.

He is not actually blaming Thor here, but stating a reason why he had to. And in the end of Captain Marvel, we see that

the The Avenger Initiative was started long ago before Iron Man takes place and he mentions that we need more superheroes rather than weapons.

So he already knew the alien stuff before The Avengers and started working on it.

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Don't forget the next part of the conversation:

THOR: My people want nothing but peace with your planet.

NICK FURY: But you're not the only people out there, are you? And, you're not the only threat. The world's filling up with people who can't be matched, they can't be controlled.

I've put in bold the part that's relevant - This can be argued to be foreshadowing of the fact that Fury clearly knows that Asgardians are not the only aliens out there.

As AJ stated:

At the end of Captain Marvel, Fury writes the proposal for the Avenger Initiative. At this point he doesn't have the Tesseract available, as it's still inside Goose (until the post credit scene anyway), so it makes sense he needs to create a team of people like Carol Danvers as a line of defence.

Once Fury has the Tesseract back however, he would be expected by the Security Council to try and use it, especially after the issue with Stark being deemed unsuitable for the Avengers. Fury is not known for giving everything away, so it is entirely possible he didn't report the full details of Captain Marvel to the higher ups, especially if he was concerned about Skrulls inhabiting other posts of influence. This also works in the Avengers, as he tells the team just enough to force them to bond together after Coulson's death, even including a lie about the cards being in Coulson's jacket to "give them a push". Fury's not a man who explains himself. He's "THE spy" whose "secrets have secrets".

Fury would want to give the Avengers a reason to explain the need to build weapons without giving everything else about Captain Marvel away and Thor's altercation with the Destroyer essentially gave him a perfect excuse to do so. He may also have believed that they had more time to follow through on the Avenger Initiative, until the Destroyer's arrival forced an acceleration to his plans.

It's not a sudden realisation that Earth is outmatched, but he plays it off like it is so he can keep his cards close to his chest.

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