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Unbeknownst to S.H.I.E.L.D., HYDRA had been infiltrating the organization for decades. Nick Fury had suspicions about the real purpose of Project Insight and secretly hired Algerian mercenary Georges Batroc and his team to hijack the Lemurian Star.
Captain America, Black Widow and STRIKE retook the ship and Romanoff downloaded the Project Insight data to a USB drive for Fury. When Fury attempted to access the drive, he was locked out, apparently by himself. Growing even more suspicious, he asked Alexander Pierce to ask the World Security Council to delay the launch of the Project Insight Helicarriers.
- "Get me off the grid!"
- ―Nick Fury
Worried about the ramifications of his discoveries, Nick Fury left the Triskelion in his SUV to meet with Maria Hill. While on his way to meet Hill, HYDRA agents, disguised as Washington, D.C. police officers, began their attack. First, they rammed and trapped Fury's SUV with their own vehicles and opened fire. This attempt failed due to the vehicle's heavy armor, so they resorted to breaking open the driver's window with an Electronic Battering Ram. The SUV window withstood three strikes before Fury attacked them with a built-in turret in his SUV. When the turret damaged, Fury was left with no choice but to attempt to escape his attackers.
However, just as Fury appeared to be successful in his escape attempt, the Winter Soldier appeared in front of him. He fired a Magnetic Disk Grenade which attached itself to the undercarriage of the SUV and exploded, flipping the vehicle over. Badly injured, Fury managed to use a mouse hole to cut himself an escape route through the street and into the sewers. From there, Fury traveled to Steve Rogers' apartment, hoping to alert him to the corruption within S.H.I.E.L.D.
Later that evening, when Steve Rogers returned to his apartment, he found Fury there. Fury explained the situation to him using code and gave him the USB drive containing the Lemurian Star file. As Fury explained the situation, however, he was shot by the Winter Soldier through the apartment wall. Sharon Carter, a S.H.I.E.L.D. Special Service agent, who was on an undercover assignment to protect Rogers, broke down the door after hearing the gunshots. She explained her role to Rogers, who told her to stay with Fury while he pursued the Winter Soldier. However, Rogers failed to stop him.
Nick Fury was brought to the hospital in Bethesda, Maryland where he apparently died. Unbeknownst to all present, Fury used a heart-slowing serum created by Bruce Banner to fake his death. Because of this, Fury was declared dead by Doctor Fine. Steve Rogers and Natasha Romanoff discussed the incident at his apartment and she explained to Rogers who the Winter Soldier was.
With Fury believed to be dead, Alexander Pierce called Rogers to his office to find out if Rogers had been told anything by Fury. Rogers denied that he had, but Pierce was not convinced and ordered STRIKE to capture him. STRIKE failed, and Rogers escaped. Knowing that Rogers would be a threat to Project Insight, he ordered a hit on Rogers and Romanoff. STRIKE and the Winter Soldier captured them and Falcon, but Maria Hill freed them and brought them to Fury.
Fury only let a select few know that he was alive, including Maria Hill, Captain America, Black Widow, Falcon, and Eric Koenig. He sent a signal to Phil Coulson via his S.H.I.E.L.D. badge with coordinates to the secret facility named Providence.
Fury saved the lives of Jemma Simmons and Leo Fitz, and assisted Coulson's Team against John Garrett in the Battle at Cybertek. In the aftermath of the battle, Fury appointed Coulson as the new director.
Still believing Fury was dead, Robert Gonzales created his own faction of S.H.I.E.L.D. When he discovered another faction led by Phil Coulson operating in a style similar to Fury's, he sent Agents Bobbi Morse, Isabelle Hartley, and Alphonso Mackenzie to infiltrate the faction, report to him, and deliver the Toolbox. Ultimately, these two factions fought in the S.H.I.E.L.D. Civil War until Coulson revealed that Nick Fury was alive,  and Gonzales accepted Coulson as Director.
- ↑ 1.0 1.1 1.2 Captain America: The Winter Soldier
- ↑ Agents of S.H.I.E.L.D.: 1.18: Providence
- ↑ Agents of S.H.I.E.L.D.: 1.20: Nothing Personal
- ↑ Agents of S.H.I.E.L.D.: 1.22: Beginning of the End
- ↑ Agents of S.H.I.E.L.D.: 2.15: One Door Closes
- ↑ Agents of S.H.I.E.L.D.: 2.19: The Dirty Half Dozen
- ↑ Agents of S.H.I.E.L.D.: 2.20: Scars