In the 1980s, S.H.I.E.L.D., NASA and the United States Air Force cooperated in a project with the goal of studying the Tesseract, led by the Kree scientist Mar-Vell working under the disguise of 'Wendy Lawson'. The project's site was the Joint NASA USAF Facility, located in the Mojave Desert. There, Lawson developed a Light-Speed Engine, a device that could help Skrulls escape the Kree, ending the Kree-Skrull War. The facility also stored the documents relating to the project.
In 1995, Starforce member Vers was stranded on Planet C-53. She allied with Nick Fury, who agreed to help her find information about the Light-Speed Engine and took her to the Joint NASA USAF Facility, where they uncovered information about Vers' past on Earth. However, Fury informed S.H.I.E.L.D of their whereabouts, unaware that they had been infiltrated by Skrulls. After he learned of his mistake, he went rogue with Vers, and they both fled the facility in a Quadjet.
Carol Danvers eventually figured the Kree's deceptions and allied herself with the Skrulls, helping Talos find Mar-Vell's Laboratory, along with a group of Skrull refugees and the Tesseract located in the lab. The Starforce chased them to the lab and captured them, but Danvers discovered her full extent of powers and defeated them all, helping Nick Fury and the Skrulls escape the lab in a Quadjet piloted by her best friend Maria Rambeau. Starforce member Minn-Erva followed them in a dropship to the Mojave Desert, where she tried to take them down in an air battle. However, she was out-maneuvered and defeated by Rambeau, who destroyed her dropship. Starforce leader Yon-Rogg then tried to shoot them down, Danvers damaged his dropship, causing him to crash-land in the Mojave Desert.
After defeating an armada of Kree forces attacking Earth outside the atmosphere, Carol Danvers went back on Earth to the Mojave Desert to face Yon-Rogg. He tried to distract her by challenging her to defeat him without using her powers, but she ignored him and incapacitated him with a photon blast. Danvers then put him back in his dropship and sent him to Hala with a message for the Supreme Intelligence.
Beginning of Project P.E.G.A.S.U.S.
The World Security Council decided to re-start a Project P.E.G.A.S.U.S. dedicated to the analysis of, and to eventually weaponize, the Tesseract, inside the Joint Dark Energy Mission Facility in the Mojave Desert. Both S.H.I.E.L.D. and NASA provided scientific expertise to the project, and due to the highly sensitive nature of the research, S.H.I.E.L.D. also provided its security force.
Recruitment of Erik Selvig
Erik Selvig, having impressed S.H.I.E.L.D. with his discoveries following Thor's arrival on Earth and the reveal of other inhabited planets that could be reached by opening stable Wormholes, was called to the Joint Dark Energy Mission Facility by Nick Fury.
Fury wanted Selvig to examine and study the Tesseract, describing it as an object belonging both to history and mythology, and a source of unlimited power. Loki, having survived his fall into Yggdrasil, became aware of the Tesseract's location on Earth, and started manipulating Selvig's decisions in order to eventually gain access to it.
Erik Selvig's First Tests
Erik Selvig received a call from Jane Foster, who wanted to consult him about data she collected to reproduce the same Wormhole that was used by Thor to come to Earth. Both Foster and Darcy Lewis noticed that something was happening to Selvig, but he dismissed them telling that he simply wasn't sleeping well, as the Tesseract was experiencing energy fluxes.
Assignment of Clint Barton
Nick Fury assigned and personally took agent Clint Barton to the Joint Dark Energy Mission Facility, with orders of both guarding the Tesseract as S.H.I.E.L.D.'s most important possession, and investigating Erik Selvig's strange behavior. Upon arriving, Selvig informed Fury of some advances made thanks to the new element discovered by Tony Stark, that allowed the scientists working in the project to create several power surges, hoping to stabilize the direct current and maintain a safe level of input and output energy over time.
Fury introduced Barton as one of his best men and departed to take a plane to the Arctic. Selvig, under Loki's influence, asked Barton if he was one of the men deployed to New Mexico a year before, as Loki noticed him then and remembered his face.
Destruction of Project P.E.G.A.S.U.S.
Nick Fury and Maria Hill arrived at the Joint Dark Energy Mission Facility in order to check a spontaneous activation of the Tesseract, that forced to apply a protocol to evacuate the facility. Phil Coulson, already stationed at the facility, was ordered to improve the evacuation time. Hill noted that the evacuation may be futile as if the Tesseract couldn't be controlled, may there couldn't be a minimum safe distance, while Fury ordered the evacuation of the technology pertaining to the project only known as Phase 2.
Erik Selvig briefed Fury about the status of the Tesseract, and how they were not ready to handle what was coming. Clint Barton informed him that none could have activated the Tesseract and that Selvig was not suspicious of anything. However, Barton noticed that, as the Tesseract was a door to the other side of the universe, it could have been activated on the other side.
During the conversation, a portal was opened and Loki appeared, coming from a distant point in space. Fury asked him to drop his Scepter, but Loki attacked without answering, killing many of the S.H.I.E.L.D. agents securing the room. However, he decided to spare Barton's life, mind-controlling him 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 the denizen of Asgard, sent with what he defined as a glorious purpose. Selvig recognized Loki as Thor's brothers 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 after realizing that the energy liberated by the Tesseract would collapse the room and probably the entire facility over them, but Barton warned Loki about the ruse. Barton shot Fury on Loki's orders and then left with Loki and the people under Loki's thrall. As the group left the facility, they passed by Hill who questioned Barton about Loki's identity. After failing to receive a substantive answer and upon being warned by Fury, who survived Barton's shot, the group was enemies, Hill pursued Barton and Loki in a vehicle. She was attacked by Loki and trapped by the facility's collapse.
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 and, although Fury was able to jump and survive its crash, he couldn't prevent Loki from finally escaping with the Tesseract.
Fury informed Hill and Coulson that the two priorities for S.H.I.E.L.D. would now be the rescue of the people trapped in the ruins of the facility, and the search of the Tesseract, as from that moment, they were at war.
Phil Coulson was kidnapped by the Centipede Project and taken to an abandoned nuclear test site in the Mojave Desert. Edison Po tortured Coulson hoping that would make him surrender and let the Theta Brain-Wave Frequency Machine unlock the real memories of Coulson's resurrection. Coulson was able to resist Po's tortures and even mocked him revealing that the memories he saw were those of a basketball match. Po revealed that if Coulson fought back the machine's process, he may not survive it, though Coulson told him that he preferred to die before revealing something to him, as he did with Michael Peterson.
Po felt no guilt over Peterson's death, as he felt that they offered him the chance to have his son unharmed and that Coulson felt so bad about it because it mirrored the death of his own father, something the Clairvoyant was able to see. Coulson discussed the veracity of the powers of the Clairvoyant, as if he was a real clairvoyant, he could have seen the answers he was looking for. Po acknowledged Coulson's statement but revealed that the Clairvoyant saw Coulson's death with detail, and the only thing he could not see is what happened to him after his death. As Coulson would not reveal any information, Po ordered one of the Centipede Soldiers to continue torturing Coulson.
Coulson was later taken to a room in order to rest between sessions, being handcuffed and chained to a bed. He managed to free himself and hid under the bed to take a guard by surprise. Coulson suffocated him and exited the room, finding he was in an abandoned ghost town in the desert. Po, who was calmly waiting outside, explained that it was a nuclear test site built in the 1940s that was spared when the Cold War ended, and that it was surrounded by hundreds of miles of desert.
One of the Centipede Soldiers grabbed Coulson before he could attack Po, and took him to the chamber to submit him to the process again, torturing him. Coulson did not lose hope that S.H.I.E.L.D. would find him before Po broke him, even though Po claimed that the Clairvoyant saw how their efforts would end.
Raina arrived and noticed how Coulson looked after hours of torture and claimed that she was tending to their Deathlok. Po told her that she must have been there to help break Coulson with her persuasion skills, but she told Po that she would not have used brute force to achieve their goals. Raina and Po were interrupted by the Clairvoyant himself, who demanded to know the progress of Coulson's interrogatory. Seeing that Po did not achieve any results, he demanded to speak to Raina, putting her in charge of the interrogatory and the whole Centipede Project, and killed Po through the phone.
- "Why would S.H.I.E.L.D. keep details of your death from you? They're your family, your only family since you've lost your mother, too. But now, after all, you've sacrificed–"
"Sacrifice is part of the job. I would give my life–"
"You didn't just give your life, you gave up your chance at a normal one, at love. And she did love you, Agent Coulson."
- ―Raina and Phil Coulson
Coulson tried to learn more about the Clairvoyant, with Raina revealing that she had never spoken to him before that day, and she was excited about it, but he gave them guidance and formulas to navigate through the changing world that S.H.I.E.L.D. has been living on for years. Raina revealed that they needed Coulson to bring back to life their Centipede Soldiers, now that they managed to make them strong, control them and instantly kill them.
Raina explained the purpose of the Theta Brain-Wave Frequency Machine and how it would help him uncover the secrets buried in his subconscious, but it would kill him if he resisted the process. Coulson told her that either he would die, or hold out until his team found him.
Raina started to persuade Coulson that both of them wanted to know the same, the secret S.H.I.E.L.D. was keeping from him, and started revealing personal information given to her by the Clairvoyant to prove his powers, such as that Coulson was denied for the answers regarding his recovery when he asked for them, that the missing memories kept him up at night. Coulson trusted the system, and that all those secrets were kept for a reason.
Raina tried to persuade Coulson again, this time with personal information regarding the loss his mother, and how his death prevented him from having a normal life, and how she knows that Audrey Nathan loved him. Coulson was visibly moved by her sole mention, and Raina asked him if he missed the things he used to with her, and told him how Nathan cried when S.H.I.E.L.D. told her that Coulson died, how they shattered her heart with a lie.
Raina finally told him that it was impossible that he couldn't have doubts and wonder about what happened in Tahiti, and Coulson replied with the trigger response implanted into his memory, revealing he could not stop saying that. Coulson finally agreed to be submitted to the machine in order to gain some answers.
Skye was able to locate the nuclear test site in the Mojave Desert using Vanchat's financials to track the different accounts used by the Centipede Project to acquire the Chitauri metal used in their devices. She informed the rest of her team, and they decided to follow Skye's lead despite Victoria Hand wanted them to assist into a major assault to one of Centipede's laboratories, with Melinda May revealing that her support to Hand's decision to relieve Skye from the investigation was a ruse to let her investigate without S.H.I.E.L.D.'s interference.
Phil Coulson has agreed to be submitted to the Theta Brain-Wave Frequency Machine, asking Raina why was she so sure that the machine would work, and she revealed that she submitted to it herself. Coulson also asked why she always used flower dresses, and she simply told him that everyone like flowers, but she was glad that he noticed it.
Skye arrived at the site and started to search for Coulson. She was ambushed by one of the Centipede Soldiers, who started to pursue her, although he was hit by the S.H.I.E.L.D. SUV driven by the rest of her team.
Raina sent another soldier, while she checked Coulson, who entered into his first memory after his death, reliving again his time in Tahiti. Coulson started to remember doctors Streiten and Goodman treating him in a dark facility, and told Raina that everything was dark.
Grant Ward battled the Centipede Soldier while the rest of the team started searching the place looking for Coulson. May defeated two guards while Ward resisted the Centipede Soldier's strong attacks. Seeing that the Night-Night Bracelet developed by Leo Fitz and Jemma Simmons had no practical use as a weapon in battle, Ward extracted the dendrotoxin capsule and managed to make the soldier swallow it, rendering him unconscious.
Coulson started remembering the different procedures made to resurrect him, and how a machine rewrote his memories while he begged the doctor to let him die. Coulson started feeling great pain and repeated the begging, allowing Skye to find him following his screams. Skye entered the room and though Raina claimed all the process was for Coulson's own good, she knocked Raina unconscious with a single punch. May disconnected the machine, and Coulson was able to recover, with a moved Skye hugging him.
Arrival of Lorelei
Asgardian criminal Lorelei wondered aimlessly through the Death Valley area of the Mojave Desert, having being able to escape from Asgard during the attack by the Dark Elves, using one of Loki's secret passageways between realms to escape to Earth. Newlyweds Jimmy and Nicole Mackenzie stopped at a roadside motel for instructions, and while Nicole entered the motel, Jimmy was approached by Lorelei, who first took his water to calm her thirst, and then started to ask about her current location, to learn if all of Midgard was as desolate as Death Valley.
Lorelei asked Mackenzie for transport out of the region, but he refused to tell her that his car was meant for two, he and his wife Nicole and advised her to ask the manager inside. Lorelei saw Nicole inside and tried to enthrall Mackenzie, asking him if he preferred Nicole to her. Mackenzie was strong enough to resist her at first, but he couldn't avoid getting enthralled as Lorelei touched him, praising his loyalty. Mackenzie departed with Lorelei, leaving his wife behind, and swearing to protect and to keep Lorelei safe.
Jimmy Mackenzie and Lorelei stopped at Rosie's Desert Oasis while traveling out of the Mojave Desert. Mackenzie went to grab some supplies for their trip, and Lorelei was approached by Rooster, leader of the biker gang Dogs of Hell. Rooster commented how a beautiful woman like Lorelei ended with a man like Mackenzie, guessing he should be rich. Lorelei casually revealed that she simply took him from his bride because she needed safe passage, and Rooster recommended her to stay there, as the area was a good place to stay unnoticed if she was in trouble.
Lorelei was shocked to see Rooster's Harley Davidson Softail, thinking it was a kind of beast, and Rooster offered to let her sit on his motorbike to feel its roar. Impressed, Lorelei asked Rooster his name, revealing that it was the alias his men gave to him. Seeing Rooster was the leader of a group of men, Lorelei enthralled Rooster to make his men serve her.
Mackenzie returned and tried to get Lorelei away from Rooster. He was hurt to see that Lorelei had replaced him even though he thought they would be together forever. Lorelei decided that his usefulness had ended, and killed Mackenzie throwing him against his car with a single blow.
Arrival of Sif
S.H.I.E.L.D. detected massive energy readings in the sky above the portion of the Mojave Desert that covers the border between California and Nevada. Jemma Simmons recognized the readings as the same kind of readings that Erik Selvig and Jane Foster detected in New Mexico and London, and therefore they heralded the arrival of an Asgardian.
S.H.I.E.L.D. ordered Phil Coulson and his team to perform an evaluation and intake of the Asgardian, although Coulson was taking "personal time" to deal with the discovery of the alien corpse used to resurrect him following the Battle of New York; Melinda May acted as the de facto leader of the team during the mission.
May traveled to the Mojave Desert with Grant Ward, Leo Fitz and a large escort of S.H.I.E.L.D. agents. Fitz detected the source of the energy in the surrounding area, and that they were getting closer to it as their convoy traveled, but he wasn't 100% sure as they still didn't fully understand Asgardian science. Ward seized the opportunity to question May about the reason Coulson suddenly changed his mind inside the Guest House about administering the GH.325 to Skye.
As Fitz detected a massive energy surge, the Bifrost Bridge transported Sif to the road right before the S.H.I.E.L.D. convoy. Fitz ran a facial recognition scanner, that compared her to the footage S.H.I.E.L.D. managed to take from the Battle of Puente Antiguo, and determined she was one of Thor's allies. May ordered the agents to stand down and approached Sif together with Ward. Sif quickly asked if they were members of S.H.I.E.L.D., something that surprised Ward, and Sif proceeded to introduce herself and ask them for assistance in finding the Asgardian criminal Lorelei.
Building an Empire
Using Rosie's Desert Oasis as a base of operations, Lorelei ordered the Dogs of Hell to steal from nearby towns searching for gold; although the bikers didn't literally fulfill her orders and stole money, jewels, weapons and everything they considered useful. Lorelei wasn't pleased when Rooster until he explained money's value. Lorelei asked her about the identity of Benjamin Franklin, who was depicted in the bills, mistaking him for an "ugly woman", and Rooster wrongly explained that he was one of the Presidents of the United States and ruled the whole country. Lorelei asked if women were able to rule, and though technically possible, Rooster told her she would be the first.
Rosie appeared wanting to know why Rooster was ignoring her calls, as she had been worried about him the whole day. Rooster explained that he simply turned off his phone because its sound bothered Lorelei. Jealous, seeing Lorelei using her clothes, and angered as his husband told her she was nobody next to Lorelei, Rosie ordered everyone to exit her bar. Lorelei, tired of the quarrel told Rooster to silence her, and Rooster simply killed his wife strangling her with his own hands.
S.H.I.E.L.D. traced the Dogs of Hell to the Rosie's Desert Oasis, and ordered Phil Coulson to lead an assault team, with the assistance of Sif, to apprehend Lorelei. They also requested the support of the local authorities, but members of the Nevada Highway Patrol were enthralled by Lorelei. Coulson, Grant Ward and Melinda May arrived at the bar with Sif, who was surprised to see that Lorelei didn't choose a castle or a palace as her base of operations as she used, though Ward informed her that she probably chose it for the men at her disposal. Enthralled Sheriff of the Nevada Highway Patrol started a firefight against the S.H.I.E.L.D. agents to protect Lorelei, and the agents used the recently created I.C.E.R.s to retaliate without damaging the enthralled men.
Lorelei was bothered by the noise of the gunshots, and Rooster informed her that law agents have arrived. Lorelei reminded he swore to fight for her, though Rooster was concerned by the amount of firepower that S.H.I.E.L.D. brought, and even a female warrior with a sword, that Lorelei instantly recognized as Sif.
Coulson asked Sif, who could withstand the gunshots, to provide them with cover, and she did it literally, moving a huge RV with a single kick to cover the agents, who then managed to knock the enthralled men down with their weapons. Coulson then ordered his men to stay outside and let Sif apprehend Lorelei, and told Ward to surround the building and guard the back exit.
Sif went inside the bar and confronted Lorelei, but she ordered his men to kill her while she escaped. Sif easily defeated the bikers, although the Asgardian Collar meant to stop Lorelei's enthrallment was damaged by a gunshot. Ward was ambushed by Rooster, and easily knocked him down, but she was confronted by Lorelei herself. Ward ordered her to surrender, but she tried to enthrall him. Ward resisted her first attempt and asked for backup, but she managed to touch him and fully enthrall him, leaving together the area and traveling to Las Vegas.