The Destruction of Project P.E.G.A.S.U.S. was the battle that had started the Chitauri Invasion. The outcome of the battle was the complete destruction of almost all the work done in the Project P.E.G.A.S.U.S. facility and Hawkeye, Erik Selvig, and other S.H.I.E.L.D. agents falling under Loki's mind control.
The events in Puente Antiguo, New Mexico spurred the World Security Council to order Nick Fury to divert the majority of S.H.I.E.L.D. resources into Project P.E.G.A.S.U.S. and Phase 2, a program designed to unlock the secrets of the Tesseract and create weapons based on their findings.
Loki was defeated by Thor and fell into Yggdrasil itself, transporting him to the Sanctuary. Loki came into contact with the Other, a servant of Thanos, who offered to make a pact that would allow him to become ruler of the Earth while Thanos would take the Tesseract. Loki accepted, and Thanos gave Loki control of the Chitauri and provided him with the Scepter that was powered by the Mind Stone. It acted as both a very powerful weapon, and also as a mind control device, bending those who were touched by the gem's power to its will.
Accepting the deal without fear of failure, Loki turned his focus back to Earth in search of a suitable agent, someone close to the Tesseract. He found Erik Selvig, a friend of Thor's and renowned astrophysicist, who had been tasked with unlocking the secrets of the mysterious cube. In time, Selvig came to understand some of the Tesseract's capabilities, and through Loki's influence, developed equipment that would focus some of that power.
When the time was right, Loki activated the Tesseract, forming a temporary portal that pulled him to its location on Earth. Despite Nick Fury asking him to lower the Scepter, Loki attacked without answering, killing many of the S.H.I.E.L.D. agents securing the room. However, he decided to spare Hawkeye's life, using the Mind Stone to gain his assistance, and went to control other agents.
Fury tried to leave with the Tesseract, and while politely asking him not to leave, Loki introduced himself as denizen of Asgard, sent with what he called a "glorious purpose." Erik Selvig recognized Loki as Thor's brother from the legends, and Fury tried to appease him, claiming Humans had nothing against the people of Asgard. Loki gave a speech about his purpose of unifying the world under his rule and controlled Selvig.
Fury tried to stall Loki, realizing that the energy liberated by the Tesseract would collapse the room and probably the entire Joint Dark Energy Mission Facility, but Barton warned Loki about the ruse. Barton shot Fury on Loki's orders and then left with him and the other people under the Frost Giant's thrall.
As the group left the facility, they passed by Deputy Director Maria Hill who questioned Barton about Loki's identity. Failing to receive a substantive answer and upon being warned by Fury, who survived Barton's shot, that the group were enemies, Hill pursued Barton and Loki in a vehicle.
Agent Phil Coulson informed Fury of the full evacuation of the facility, and Fury himself managed to board a helicopter before the ground collapsed. Meanwhile, Barton managed to escape Hill after she was trapped by debris falling from the tunnel as it collapsed, but his vehicle was pursued and attacked by Fury's helicopter. Loki shot at the helicopter with his scepter and, although Fury was able to jump and survive its crash, he could not prevent Loki from finally escaping with the Tesseract.
Now that Loki had started a war, Nick Fury decided this warranted the reactivation of the Avengers Initiative. One by one, Bruce Banner, Tony Stark, and Steve Rogers came together. When Thor managed to return to Earth, he joined as well.