- "We only get one shot at this, so let's go over the plan one more time to make sure we're clear on exactly what we're doing, okay? Trip and I will crest the ridge, use a noisemaker to grab a three-wheel, maybe something with more fireworks and open a window for you two. You crawl in, grab the dealer, force his hand. He'll get us our ace in the hole and then Bob's your uncle."
- ―Phil Coulson to his team
During the HYDRA Uprising, it was learned by Phil Coulson that his old colleague John Garrett was both a HYDRA sleeper agent and the Clairvoyant. They were both trained by Nick Fury. Previously, Garrett had become patient zero of Project Deathlok from his injuries in a mission, but when his organs began to fail, he sought the secret to Coulson's resurrection in order to save himself. After Leo Fitz used an EMP to damage Garrett's cybernetics, Raina injected him with a synthetic version of GH.325, which restored and strengthened him. Fitz, along with Jemma Simmons, was ejected from the Bus in a Medical Pod into the Atlantic Ocean by Grant Ward.
Meanwhile, Ward, a trainee of Garrett, was discovered to be a sleeper agent as well. During his time with Coulson's Team, he became a trusted agent, had a sexual relationship with Melinda May, and confessed his feelings for the new recruit and his trainee, Skye. Coulson's team was devastated by his betrayal; May and Skye discussed their reaction. Ward stole the Bus and was using it as a transport plane for himself and members of the Centipede Project.
Ian Quinn was freed from the Fridge by Garrett and Ward,  and met with representatives of the United States Armed Forces to offer them a thousand Deathlok Soldiers to compensate for the downfall of S.H.I.E.L.D. and to assist with the War on Terror. Quinn, to close the deal, offered to give a tour of the Cybertek Manufacturing Facility to show them their product.
Coulson's Team wanted to bring the criminals to justice and retrieve the Bus. After a battle that destroyed the Barbershop Headquarters in Cuba, Coulson's team found Garrett in New Mexico by using the tracker Fitz and Simmons placed on the Bus.
Phil Coulson paired up with Antoine Triplett, and used a Noisemaker to distract the Cybertek guards. This helped them obtain a Humvee, which assisted Skye and Melinda May in blowing a hole through one of the building's walls. The representatives of the United States Armed Forces heard the gunfire, but as Ian Quinn attempted to quell their fears, John Garrett, Deathlok, and Grant Ward entered. Garrett proceeded to kill General Jacobs, while Ward captured the other representatives. Meanwhile, May and Skye entered the Centipede Soldier Control Center of Cybertek and threatened the handlers with a bomb. During a conversation with Kyle Zeller, they let him know they had control. Skye then called Garrett to let him know Coulson was coming for him. Garrett bragged about the deaths of Leo Fitz and Jemma Simmons, while Ward was instructed to apprehend Skye. Deathlok was ordered not to leave Garrett's side.
Unknown to Garrett, Fitz and Simmons were saved by Nick Fury who was seeking Coulson; eventually, Fury discovered his location.
When Ward confronted Skye, May attacked and their fight wound up crossing over into the neighboring construction site. Although Ward maintained the upper hand throughout the fight and was about to finish her off, May ultimately won by shooting Ward in the foot with a nail gun and crushing his larynx.
As Deathlok and Garrett heard the noisemaker, Coulson found Garrett, who easily smacked Coulson across the room. Before he could be defeated however, Fury arrived and gave Coulson the Destroyer Armor Prototype Gun , as Centipede-enhanced soldiers began firing on them. Coulson took out the soldiers as Fury fired on Garrett. When Garrett ordered Deathlok to attack, he deployed his Forearm Rocket Launcher.
Before he could fire, his new handler, Skye, had freed Ace Peterson. Knowing his son was safe, Deathlok fired upon Garrett and, as Garrett begged for Coulson to stop him, Peterson stomped him with his prosthetic leg.
- "Before it was torn apart, S.H.I.E.L.D. was a lot of moving parts. Guys like you were the heart. Now... you'll be the head."
"What is it?"
"A toolbox to help you build it back up."
"You want me to start over, rebuild S.H.I.E.L.D."
"From scratch. Take your time and do it right."
- ―Nick Fury and Phil Coulson
Nick Fury appointed Phil Coulson as his successor as director of S.H.I.E.L.D. and tasked him to rebuild the organization from scratch. To that end, Fury gave Coulson the Toolbox, which included a map that led to the Playground and its guardian, Billy Koenig, before Fury decided to leave for Europe.
Cybertek's hostages were freed, including Ace Peterson, who was reunited with his aunt. Deathlok chose to venture on his own, seeking redemption.
Centipede-enhanced soldiers, many of whom were forced into servitude by the Incentives program, were promised the removal of the Backscatter X-Ray Eye Implants.
Grant Ward was arrested and promised to be tortured mentally and physically by Coulson and May, respectively, for what he did to them and Fitz, specifically.
- ↑ Agents of S.H.I.E.L.D.: 2.12: Who You Really Are
- ↑ 2.0 2.1 2.2 Captain America: The Winter Soldier
- ↑ Agents of S.H.I.E.L.D.: 5.18: All Roads Lead...
- ↑ Captain America: The Winter Soldier takes place two years after The Avengers
- ↑ Agents of S.H.I.E.L.D.: 2.01: Shadows
- ↑ 6.0 6.1 Agents of S.H.I.E.L.D.: 1.17: Turn, Turn, Turn
- ↑ Agents of S.H.I.E.L.D.: 1.16: End of the Beginning
- ↑ 8.0 8.1 8.2 8.3 8.4 Agents of S.H.I.E.L.D.: 1.21: Ragtag
- ↑ Agents of S.H.I.E.L.D.: 1.12: Seeds
- ↑ Agents of S.H.I.E.L.D.: 1.15: Yes Men
- ↑ 11.0 11.1 Agents of S.H.I.E.L.D.: 1.19: The Only Light in the Darkness
- ↑ 12.0 12.1 Agents of S.H.I.E.L.D.: 1.18: Providence
- ↑ 13.0 13.1 13.2 13.3 13.4 Agents of S.H.I.E.L.D.: 1.22: Beginning of the End