The Centipede Project is a super-soldier program organized and funded by HYDRA.
The Centipede Project is a HYDRA funded science program with the stated purpose of creating an army of super-powered soldiers for their cause and finding the means to bring them back from the dead when necessary. However, the project's leader, John Garrett, saw it as a means of restoring his own failing health.
In 2010, they acquired captured Akela Amador from Vanchat, who was holding her captive after she led a botched raid on one of Vanchat's gulags. Amador's captors installed a Backscatter X-Ray Eye Implant in Amador through which they controlled her. They would give her assignments through the eye and insured her loyalty by way of a kill switch that they would activate at the first sign of treachery or capture. These eye-devices are how they ensure the loyalty of all of their operatives. Amador's handler and Centipede's enhanced soldiers are known to have had these eyes installed.
The project's scientists created the Centipede Serum, derived from a variation of the Super Soldier Serum, mixed with Gamma Radiation and the newly-discovered Extremis formula, as a means of granting powers to their subjects, but their initial results were highly unstable with explosive results.
When Phil Coulson, was slain before the Battle of New York and restored to life days later through means unknown, Garrett felt discovering the truth about Coulson's return was the key to both the Centipede Project and to restoring his increasingly failing health.
The Project came to the attention of S.H.I.E.L.D. as Phil Coulson and his team arrived at Los Angeles were investigating the case of Michael Peterson who was Debbie's test subject. Debbie had administered the Centipede Serum through a Centipede Device to Peterson and another test-subject. When that other test subject exploded due to Centipede's use of the unstable Extremis process, Peterson saved Debbie from the destruction of the lab in a public display of his powers. Debbie was furious with him told him to disappear or else he would compromise the secrecy of the project.
When Peterson seemed also on the verge of destabilizing, Debbie dispatched an assassin to ensure his silence. The assassin was stopped by Melinda May and Peterson was taken off the grid by Leo Fitz and Jemma Simmons, who managed to stabilize the Extremis reaction.
Stockholm and Belarus
Soon after, Centipede sent Akela Amador on a series of diamond thefts in order to reach the $30 million asking price for a prox card that would allow access to the Todorov Building in Zloda, Belarus. When Coulson heard about the crimes, he suspected Amador and requested the assignment. Coulson and his team tracked Amador from Sweden to Belarus and was able to take her into custody without her handler realizing.
Coulson's Team managed to isolate the signal to the eye, which allowed Grant Ward to carry out Amador's mission, while Jemma Simmons and Leo Fitz performed ocular surgery on Amador to remove the Backscatter X-Ray Eye Implant. Ward successfully completed Amador's mission by infiltrating the research facility and observing and transmitting a series of symbols written on a chalkboard back to Centipede.
Using Miles Lydon's assistance, the Project managed to locate S.H.I.E.L.D. Index-registered pyrokinetic Chan Ho Yin. In Hong Kong, Raina ordered two Project's employees to abduct Chan from his apartment. Chan was brought to the Hong Kong Centipede Base where Debbie harvested the fire-resistant platelets in Chan's blood. The platelets allowed the Extremis element of the Centipede Serum to be stabilized without the explosive after-effects. Having gotten what they needed from him, Debbie ordered Chan to be drained, killing him.
But before that could happen, Chan was released by a S.H.I.E.L.D. extraction team led by Phil Coulson and Quan Chen. Unfortunately, Chan was tired of S.H.I.E.L.D.'s interference in his life and killed Quan. Chan then confronted Debbie and Raina. Raina abandoned Debbie, leaving her to be incinerated by Chan. Raina escaped, but the lab was destroyed when Chan detonated from an Extremis over-dose. Before the destruction of the lab, Skye managed to extract a few files from the building's mainframe, hopefully enough to give S.H.I.E.L.D some new leads on their activities.
Upon the end of her mission in Hong Kong, Raina arrived at the Havenworth Federal Penitentiary speaking to Edison Po. Raina informed Po that with the stabilization of the Centipede Serum, "Stage One" of the project (the stabilization of the formula) had been completed and that they were moving into "Stage Two" (the creation of super-soldiers). She also passed along the request of the Project's leaders that Po contact Clairvoyant for any insights he might have as to "Stage Three" of the project.
Oakland and Long Beach
Edison Po was soon broken out of the facility by a squadron of Centipede Soldiers. They took him to the new Centipede lab in Oakland, California, where Raina updated him on the project's status. Po determined that Coulson's Team presented a threat that needed to be taken care of. To this end, he set a trap for Coulson and his team with three Centipede soldiers prepared for an ambush. However, Coulson had recruited Michael Peterson who turned the tide against the soldiers, but it also gave Po and Raina the inspiration for a plan of action.
Po had previously contacted the Clairvoyant, who claimed that he had trouble seeing the man that Centipede needed, the man who held the key to "Stage Three", and his weaknesses. After seeing Coulson, Po realized that he is exactly the man that the Clairvoyant couldn't see and hold the key to "Stage Three".
Raina kidnapped Ace Peterson and threatened to have him killed if Peterson didn't obey her instructions. Believing that Centipede wanted to exchange Peterson for his son, Coulson accompanied Peterson to the exchange site in Long Beach, California. Seeing no other way to save his son, Peterson betrayed Coulson to Raina. After seeing to his son's safety, Peterson tried to make up for his actions by returning to rescue Coulson, but he was seemingly killed in an explosion.
Raina escaped the scene with Coulson by way of helicopter. Upon leaving the scene, Raina explained to Coulson that their true interest was in the nature of Coulson's mysterious revival after his "death", as this is seemingly the key to "Stage Three" of the Project's plans.
Phil Coulson was taken to an abandoned nuclear testing grounds in the Mojave Desert, where Edison Po attempted to gain the secret of Coulson's survival while Raina saw to the recovery of Michael Peterson who survived the explosion in Long Beach, albeit with severe injuries. When Po's interrogation techniques proved ineffective, the Clairvoyant expressed his dissatisfaction by executing Po and giving the job of discovering Coulson's secrets to Raina. Raina managed to convince Coulson not to resist the process and let the machine do its work.
Meanwhile, S.H.I.E.L.D. was leaving no stone unturned in their search for Coulson. A sting operation performed by Coulson's Team under the direction of Victoria Hand netted Vanchat who had had dealings with Centipede in the past. Between the Intel gained from Vanchat, as well as an independent study of Vanchat's finances by Skye, S.H.I.E.L.D. determined the locations of several Centipede operations around the globe, as well as the Mojave location.
While S.H.I.E.L.D. struck simultaneously at multiple Centipede locations across the globe, Coulson's team headed to Mojave to rescue Coulson. After subduing a cadre of Centipede Soldiers, Coulson was rescued without giving Raina any important information about his resurrection, and Raina was taken into custody.
With a severe blow dealt with Centipede operations, S.H.I.E.L.D.'s efforts began to focus on finding the Clairvoyant. However, unknown to S.H.I.E.L.D., Michael Peterson survived and had been outfitted with a Backscatter X-Ray Eye Implant under Garrett's orders, who had started to give him assignments. Soon after, Coulson learned that Ian Quinn was in league with the Clairvoyant.
Incident in Italy
In an attempt to locate the Clairvoyant through his association with Ian Quinn, Phil Coulson and his team tracked down a $10 million dollar purchase between Quinn and Cybertek Industries. Coulson believed that Quinn would take possession of the purchase himself in Italy, and planned an undercover op for himself and his team on the train making the delivery.
Despite being sold out by Luca Russo, Coulson and his team tracked Quinn down at a private estate. However, Garrett had been tipped off on the team's arrival. After allowing her to learn of the survival of Michael Peterson, now known as the Deathlok, Garrett ordered Quinn to shoot Skye twice in the stomach before surrendering himself to Coulson.
The Guest House
When Skye's condition deteriorated, Phil Coulson decided to actively seek out the secrets behind his resurrection that had been denied him in order to save Skye. Still hoping to gain the secret of Phil Coulson's resurrection for himself, John Garrett decided to join in the hunt with Coulson in order to keep his secret from exposing. Playing on their long friendship and years serving together in S.H.I.E.L.D., Garrett arrived on the Bus on the pretense of having orders to take Ian Quinn into custody, and soon had Coulson's full confidence in the investigation.
Garrett joined Coulson and his team on a raid on the Guest House, the facility where Coulson was treated for his fatal wounds, in hopes of finding the drug that regenerated him. Before the facility was destroyed, Garrett managed to procure many of the exotic drugs and compounds stored there, but Coulson only found one sample of the GH.325 that he sought, which Coulson used to save Skye.
Hoping to end Phil Coulson's investigations into the Clairvoyant once and for all, John Garrett arranged a number of false leads generated from the rejects from S.H.I.E.L.D.'s Index of gifted individuals. Garrett used Deathlok to lead Coulson's Team to Thomas Nash was in a vegetative state and speaking through a computer. The computer's voice then "confessed" that Nash was the Clairvoyant. However, before Coulson could take Nash into custody, Nash was killed by Grant Ward, effectively ending the Centipede Investigation.
Into the Light
With the onset of the HYDRA Uprising, John Garrett's identity as the Clairvoyant was revealed and Centipede's ties to HYDRA exposed. Garrett was taken into custody by S.H.I.E.L.D., but was freed by Grant Ward, who killed Victoria Hand and released his mentor.
Now operating openly, John Garrett arranged for the release of Raina and put her in charge of the reborn Centipede Project. Garrett supplied Raina with all of the money, equipment, and resources necessary for the completion of "Phase Three" of the Centipede project which was the healing the mortally wounded and bringing the dead back to life.
Garrett supplied Raina with cadavers and the various drugs that he confiscated from the Guest House, but without the specific GH.325 drug used on Phil Coulson and Skye, her initial efforts were unsuccessful. However, after receiving the information on Skye's encrypted hard-drive, she managed to synthesize one, and only one, a vial of GH.325 using the various alien compounds that she did have on hand.
While in the process of moving the Centipede Project from Cuba to the United States on the captured Bus, Grant Ward captured Leo Fitz and Jemma Simmons, who were tracking the Bus on behalf of Coulson. Once inside the plane, Fitz activated a EMP Joy Buzzer, which shut down Garrett's mechanical systems. On the verge of death, Garrett instructed Raina to administer the synthesized GH.325 to him. In the meantime, Ian Quinn traveled to Washington, D.C. with intent of selling an army of Centipede Serum-powered, cybernetically enhanced Deathlok Soldiers to the United States Armed Forces.
While Quinn was giving a tour of the Cybertek Manufacturing Facility in New Mexico, Coulson's Team began the Battle at Cybertek to capture John Garrett and Grant Ward. It was discovered that Cybertek, in cooperation with HYDRA, had created an incentive program in which people worked as handlers because their relatives were hostages. Ultimately, thanks to the efforts of Coulson's Team and Nick Fury, the hostages were freed, Garrett was killed, Ward was arrested, and Quinn, with Raina, abandoned the Centipede Project.