John Garrett was dying. The cybernetic implants given to him by Cybertek were no longer working efficiently to keep him alive. Garrett took the moniker "Clairvoyant" and created the Centipede Project to find a way to extend his life.
In the Attack on the Helicarrier, Loki killed the S.H.I.E.L.D. agent Phil Coulson; however, Coulson was resurrected and was given his own team of agents to investigate mysterious incidents around the world. However, only those involved and high-leveled agents such as Maria Hill knew the details of how Coulson was alive.
The first mission of Coulson's team was saving the life of Mike Peterson from exploding from the Extremis portion of the Centipede Serum. Peterson was recruited by S.H.I.E.L.D. and his son Ace was sent to his aunt Mindy.
In order to gain access to the information that Phil Coulson could have about his own resurrection, Centipede Project staged a meeting by kidnapping Michael Peterson's son, Ace, to force him to hand over Coulson, making it appear he was going to surrender himself in exchange of his son's safety.
Coulson and his team took positions at a bridge near the port of Long Beach, designated as the location of the exchange, with Grant Ward acting as a sniper and the rest of the team staying behind as backup, in order to track Peterson using a Tracking Scent developed by Jemma Simmons.
Despite Melinda May's insistence to escort Peterson during the exchange, Coulson went himself as Peterson requested him, and he needed May to take point of the team if things did not go as planned. Simmons applied the scent on Peterson's hand as Leo Fitz explained to him how they would track him when the exchange was finished.
Raina appeared escorted by the Centipede Soldiers, hiding out of Ward's sight behind a concrete mixer truck, and greeted Peterson as if he were an old friend, and tried to introduce herself to Coulson. Raina thanked Peterson for fulfilling his end of the deal and delivering Coulson in exchange for his son.
Peterson become enraged for allowing such a reprobable act, and took Raina by her neck, threatening her to liberate his son in exchange for his life, but as her employer did not care for her life, if she died, Ace would die too. Coulson agreed to go with Raina in exchange for Ace's freedom. Peterson apologized to Coulson, and let Raina go.
Ace was liberated, and his father took him to Skye in order to protect him, while Coulson was sedated to be taken without resistance. May ordered Ward not to engage or they could end up killing Coulson, and she contacted S.H.I.E.L.D. Headquarters to know how to proceed.
Peterson told his son to stay with Skye while he did the right thing. However, as he approached the bridge again, an explosion occurred, seemingly killing Peterson, while Raina and the Centipede Soldiers departed with Coulson in a helicopter, attacking Ward before leaving.
Flying over the city, Raina revealed to Coulson that they wanted to know what happened after his death.
Skye was relieved from helping with the investigation of the kidnapping of Phil Coulson by Victoria Hand, a decision supported by Melinda May. The rest of her team helped her to escape the days of debrief ordered by Hand, so that Skye could conduct her own investigation regarding Vanchat's financials to locate Centipede and Coulson.
Skye tried to hack into S.H.I.E.L.D. databases from a Internet café. However, the Tracking Bracelet she was wearing had restricted her access to technology, and all the computers in the café were blocked by S.H.I.E.L.D. She quickly found another way of investigating the financials through Lloyd Rathman, a senior executive of a company investigated by the Federal Government for tax-dodging.
Skye stole Rathman's car and faked an accident to figure out his address, and she was transported to Rathman's house, where she called to his office to know when he would return home, masquerading as a member of the Los Angeles Police Department with a report of his stolen car.
Skye investigated Rathman while waiting for him, and posed as Melinda May to make Rathman help her hack into the bank accounts by using his private corporate I.D. In order to gain his assistance, Skye told him that S.H.I.E.L.D. had evidence that his company had been siphoning funds into offshore accounts for some clients, and threatened him to freeze all of his assets. She offered him a false offer of retiring the charges if he helped her, otherwise he would spent the next five years in the Fridge.
Rathman tried to gain some time until his private security agents appeared, as he activated a silent alarm, asking to see Skye's badge, as letting her enter into a Swiss bank account with his private corporate I.D. was a crime. Skye locked Rathman's phone using her Tracking Bracelet and revealed some data she obtained to make her identity even more believable, such as her knowledge of his gambling addiction and his divorces and of his account in the Cayman Islands
Skye easily disarmed the two private security agents, and Rathman started to cooperate. However, it soon became apparent that he had no idea of how to navigate through the bank accounts, as his assistant usually did that for him. One of the security agents had to act under Skye's guidance to obtain the information, managing to backtrack the large payments into Vanchat's accounts to the buyer's account, using it to track him down.
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 might not survive it, though Coulson told him that he preferred to die before revealing something to him, like 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; if he were a real clairvoyant, he could have seen the answers he sought. Po acknowledged Coulson's statement, but revealed that the Clairvoyant saw Coulson's death with detail, and the only thing he could not see was 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 other subject. 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 interrogation. Seeing that Po did not achieve any results, he demanded to speak to Raina, putting her in charge of the interrogation 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
Raina acted more friendly towards Phil Coulson than Edison Po, offering him a glass of water, although Coulson was not deceived, as he saw what happened to Po, even though Raina claimed he was just a murderer incapable of remorse. He reminded her what happened to Mike Peterson and Chan Ho Yin, though Raina said she gave them what they asked for, as Peterson wanted to be a hero for his son, but she did not answer when Coulson asked if Akela Amador also wanted a bomb in her head, replying instead that S.H.I.E.L.D. had also used cruel means to achieve its ends.
Coulson tried to learn more about the Clairvoyant, with Raina revealing that she had never spoke to him before that day, and she was excited for it, but he gave them guidance and formulas to navigate through the changing world that S.H.I.E.L.D. have been living on for years. Raina revealed that they needed Coulson to bring their Centipede Soldiers back to life, now that they had 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 information, 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 of his mother, and how his death prevented him from having a normal life, and how she knew 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 could not 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 wanting 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, having agreed to be submitted to the Theta Brain-Wave Frequency Machine, asked Raina why was she so sure that the machine would work, and she revealed that she had submitted to it herself. Coulson also asked why she always used flower dresses, and she simply told him that everyone liked 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 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 a great pain and repeated the begging, allowing Skye to find him following his screams.
Skye entered the room and, though Raina claimed all the processes were 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.
- "After New York, you weren't dead for eight seconds or forty seconds or whatever they put in your file. You were dead for... days."
"It should be, but Director Fury moved heaven and Earth. He had a team of scientists working around the clock using procedures that no good doctor would ever allow."
- ―Streiten and Phil Coulson
Raina was arrested and the Theta Brain-Wave Frequency Machine would come under S.H.I.E.L.D. possession. Though Raina believed that "Phase Three" of the Centipede Project was a failure since she did not retrieve any useful information from Coulson, Garrett, upon having her freed from prison, assured her that "Phase Three" would continue with her leading it, due to his successful Raid of the Guest House.
The Clairvoyant was now on S.H.I.E.L.D.'s radar; a Search for the Clairvoyant would begin to end his schemes. Since Edison Po quoted Coulson's psychological evaluations and Raina knew about Coulson's dating habits, Skye and Coulson figured out that the Clairvoyant was a S.H.I.E.L.D. agent. When John Garrett revealed that he knew details about the kidnapping that Coulson had not shared, his cover was blown.
Coulson went to Bethesda, Maryland and personally spoke to Doctor Streiten about his resurrection. Coulson wanted to talk to Nick Fury, but the HYDRA Uprising began before he could meet with him at the Triskelion.
- ↑ Agents of S.H.I.E.L.D.: 1.12: Seeds
- ↑ Agents of S.H.I.E.L.D.: 1.21: Ragtag
- ↑ The Avengers
- ↑ Agents of S.H.I.E.L.D.: 1.01: Pilot
- ↑ Agents of S.H.I.E.L.D.: 1.05: Girl in the Flower Dress
- ↑ 6.0 6.1 Agents of S.H.I.E.L.D.: 1.10: The Bridge
- ↑ 7.0 7.1 7.2 7.3 7.4 7.5 7.6 Agents of S.H.I.E.L.D.: 1.11: The Magical Place
- ↑ Agents of S.H.I.E.L.D.: 1.18: Providence
- ↑ Agents of S.H.I.E.L.D.: 1.19: The Only Light in the Darkness
- ↑ 10.0 10.1 10.2 Agents of S.H.I.E.L.D.: 1.16: End of the Beginning
- ↑ Agents of S.H.I.E.L.D.: 1.17: Turn, Turn, Turn
- ↑ Agents of S.H.I.E.L.D.: 1.22: Beginning of the End