How did Nick Fury become the head of the SHIELD?

Question

How did Nick Fury become the head of the SHIELD? In Captain Marvel, Nick Fury in 1995 seems to be just a Field Agent. How did he become the director of the SHIELD before 2008 (Iron Man Easter egg). He only took less than 13 years to become director from agent. For a normal agent, is his promotion too fast? What happened during this period?

Answer 1

Not much is known of Fury’s life and his experiences at SHIELD that I’m aware of. However we do find out why he was made director and who it was done by. Alexander Pierce was the head of SHIELD but when he was promoted out of it he made Fury director because of his personality and actions in Bogota.

Alexander Pierce: That photo was taken five years after Nick and I met. When I was at State Department in Bogota. ELN rebels took the embassy, and security got me out, but the rebels took hostages. Nick was deputy chief for the SHIELD station there. And he comes to me with a plan. He wants to storm the building through the sewers. I said, "No, we'll negotiate." Turned out the ELN didn't negotiate, so they put out a kill order. They stormed the basement, and what did they find? They find it empty. Nick had ignored my direct order and carried out an unauthorized military operation on foreign soil. He saved the lives of a dozen political officers, including my daughter.

Steve Rogers: So you gave him a promotion.

Alexander Pierce: I've never had any cause to regret it.

_{Captain America: The Winter Soldier}

Nick Fury: So why make me head of SHIELD?

Alexander Pierce: Cause you were the best and the most ruthless person I ever met.

Nick Fury: I did what I did to protect people.

Alexander Pierce: Our enemies are your enemies, Nick. Disorder, war. It's just a matter of time before a dirty bomb goes off in Moscow, or an EMP fries Chicago. Diplomacy? Holding action, a band-aid. And you know where I learned that; Bogota. You didn't ask, you just did what had to be done. I can bring order to the lives of seven billion people by sacrificing twenty million. It's the next step, Nick, if you have the courage to take it.

_{Captain America: The Winter Soldier}

Answer 2

Because of Fury's Skrull spy network.

In 1995, Fury encountered some Skrull refugees (introduced in Captain Marvel) who had escaped from the Kree-Skrull War. He recruited some of them to help him “keep [Earth] safe” from any potential threats, as revealed in Secret Invasion S01E02 “Promises”.

One of these Skrulls was Talos, a former Skrull general who had befriended Fury and impersonated him on several occasions. In Secret Invasion S01E03 “Betrayed”, Talos disclosed that Fury was a “benchwarming nobody in SHIELD” in 1995, and that he only rose through the ranks with the assistance of Talos and his fellow Skrulls.

Relevant dialogue:

Fury: Almost ever since I met Talos, I believed that humans and Skrulls can help each other.
The world is facing a serious threat. And I could use your help.
It would mean putting on a new face and keeping it.
This is the promise. While you work to keep my home safe, Carol Danvers and I will find you a new one.
Who'll be first to take the pledge?

^{- Secret Invasion S01E02 “Promises”}

Talos: When I came here in 1995, you were just a benchwarming nobody in a dumpy field office in S.H.I.E.L.D.
Fury: Benchwarming?
Talos: What, do you have a different take on this?
Fury: I was ascending the ranks.
Talos: You didn't start ascending the ranks until me and 19 of my people signed on as your invisible spy network.
You know, we fed you more dirt and intel than you could've uncovered on your own in a lifetime, so please.
I mean, every time you were promoted inside S.H.I.E.L.D., we did that.
Every terror attack you prevented, we did that. Every enemy you sabotaged and ally you leveraged with dirt no one else in the world had access to, we did that.

^{- Secret Invasion S01E03 “Betrayed”}