The Avengers Initiative (a.k.a Phase 1; originally conceptualized as the Protector Initiative) was a secret project created by S.H.I.E.L.D. to create the Avengers, a response team comprised of the most able individuals humankind has to offer. The Initiative will defend Earth from imminent global threats that are beyond the war-fighting capability of conventional military forces.
The Initiative was scrapped by the World Security Council after the alien incursion in New Mexico in favor of a weapons development program known as Phase 2. It was eventually reactivated in 2012 during the Chitauri Invasion.
In 1995, S.H.I.E.L.D. was involved in the conflict with the Kree and the Skrulls, and Nick Fury teamed up with Carol Danvers to save the Skrulls from the Kree and retrieve the Tesseract.
Having been inspired by Danvers and witnessing firsthand how humanity is not capable of dealing with intergalactic threats, Fury became determined to protect the Earth from more intergalactic threats like the Kree. He sought to find individuals with incredible powers and abilities just like Danvers in hopes of bringing them together as a team to fight as Earth's protectors.
The initiative was originally named "The Protector Initiative", however, after Fury saw Danvers' call-sign from the time when she was in the United States Air Force, he renamed it into the Avengers Initiative.
While S.H.I.E.L.D. was devoting a majority of its resources into the building of the Triskelion, Nick Fury used finances to observe individuals who possibly had superpowers, sending agents to investigate these individuals and have them placed on the Index for later encounters.
In 2008, Phil Coulson and Melinda May discussed the initiative enacted by Fury as they went to Manama, Bahrain to investigate Eva Belyakov. Fury had also included two of S.H.I.E.L.D. most elite agents, Natasha Romanoff and Clint Barton, for the Avengers Initiative due to their unique and incredible skills that rank them above other agents.
Tony Stark went home after he publicly announced he was Iron Man, only to find Nick Fury already there. Fury went to find Stark to inform him that there was an entire world of incredible people, just like him, and of the Avengers Initiative.
After meeting with Jasper Sitwell in a cafe, Phil Coulson informed him that the World Security Council had accepted the Avengers Initiative, but had ordered the Abomination to join the team roster, as they were blaming Hulk for the destruction in New York City. They ended up sending Tony Stark to meet with Thaddeus Ross and convinced him to refuse Abomination's admission into the project, as well as attempted to recruit Hulk into the team.
Closing the Project
Nick Fury decided that, after reading Black Widow's review about him, Stark was not fit to join the Avengers Initiative, though the Iron Man armor was. The Avengers Initiative was scrapped soon after by the World Security Council after the alien incursion in New Mexico in favor of a weapons development program known as Phase 2.
Search for Captain America
Sixty-six years after Captain America's crash landing, a S.H.I.E.L.D. team led by Fury searched for his body. A fan of the Captain, Coulson, was also part of this small team. The team searched for two years to find Rogers' body. When they finally found him, they defrosted him and then shipped his body to New York City. When Rogers arrived in New York City, he was kept in a simulated 1942 environment to try to ease him into what was happening.
When he awoke, he quickly realized it was not real and escaped into the streets of a 2011 New York. In Times Square, Rogers encountered Fury who told him that he's been "asleep" for nearly seventy years. Rogers then realized that many of his old friends were very likely dead, including his love interest, Peggy Carter.
Testing The Database
Clint Barton was ordered by Nick Fury to break into the Helicarrier and access the database of the Avengers Initiative to test their security. Barton was able to accomplish this easily, and after looking over Fury's report on the candidates, he questioned Fury on their reliability, which Fury assured him that they needed to count on them.
Loki stole the Tesseract from Project P.E.G.A.S.U.S., and destroyed the base, killing eighty people during the process, causing Nick Fury to revive the project. He called in Captain America to join, and sent Black Widow to get Hulk, who was now living in a rural village in India. Meanwhile, Phil Coulson was sent to Stark Tower to retrieve Tony Stark.
Thor returned to Earth from Asgard in order to get his adopted brother.
After the Avengers were formed, they were not cooperating and failed to prevent Loki's escape from the Helicarrier. They believed they were not meant to be together and were thinking of disbanding the team. It was only Phil Coulson's death that motivated them to fight the Chitauri invasion on New York City. After their victory in defeating the Chitauri, Nick Fury and Maria Hill agree that it was the correct choice to form the team and that they will return for any future threat.