Battle at the Triskelion

"Hey, Cap, how do we know the good guys from the bad guys?" "If they're shooting at you, they're bad."

- Falcon and Captain America

The Battle at the Triskelion, also referred as the Fall of S.H.I.E.L.D., was the first open battle between HYDRA and S.H.I.E.L.D., and a major event during the HYDRA Uprising. After HYDRA, thought dormant since the end of World War II in Europe, was revealed to be active inside of S.H.I.E.L.D., Nick Fury faked his death following an assassination attempt and recruited Captain America, Black Widow and Falcon to fight against the resurgent terrorist group. The Winter Soldier fought alongside his HYDRA captors while he was brainwashed.

Background
The attack on Nick Fury caused Captain America to become a fugitive from S.H.I.E.L.D. by order of Alexander Pierce, because Rogers would not give Pierce the USB drive that Fury had entrusted to Rogers. This drive was recovered by Black Widow and given to Fury after the hijacking of the Lemurian Star.

Natasha Romanoff became a fugitive for assisting Rogers and decrypting the USB drive at Camp Lehigh. There she and Rogers learned the secret of S.H.I.E.L.D. from Arnim Zola: HYDRA had been rebuilt inside of the law-enforcement agency, operating clandestinely within its ranks and wreaking havoc across the globe. This insidious resurgence had been in progress since the collapse of the Red Skull's initial incarnation, following his apparent death at the hands of Captain America.

The two needed an uncompromised ally, so they recruited Sam Wilson, a United States Air Force Special Operations Pararescueman who could get access to mechanical wings.

The Winter Soldier, a legend in the espionage community, was revealed to be none other than Bucky Barnes, Steve Rogers' long-lost best friend. Barnes was incorrectly believed to be killed in action following a raid on a HYDRA train in late 1944. Pierce invited the World Security Council to Washington, D.C. to witness the launch of Project Insight, a project of S.H.I.E.L.D., corrupted by HYDRA, that would preemptively locate and fire upon dangerous targets by three next-generation Helicarriers.

Battle
"I can bring order to the lives of seven billion people by sacrificing 20 million. It's the next step, Nick. If you have the courage to take it." "No. I have the courage not to."

- Alexander Pierce and Nick Fury

The battle began when Captain America, Falcon and Maria Hill infiltrated the Triskelion's communications room. Rogers then used the intercom to notify all of the agents and employees in the building of HYDRA's plot, urging them to stop the launching of the Helicarriers. HYDRA agent Brock Rumlow ordered the launch be preempted in response, but the technician refused. Agent Sharon Carter pulled her sidearm on Rumlow, who cut her hand with his knife and stole her gun after a tense Mexican Standoff, involving numerous HYDRA and loyal S.H.I.E.L.D. agents. This action caused the a shootout between the two factions, during which Rumlow was able to escape. Rogers and Falcon then boarded the Helicarriers as they were beginning their takeoffs.

Meanwhile, in the World Security Council room, Alexander Pierce's identity had been revealed to the other council members due to Rogers' speech. The council members were even more shocked when STRIKE agents loyal to HYDRA filled the room and held them all at gunpoint. Pierce then asked Councilman Singh if he would be so against Project's Insight's true goals if the same methods were used to save his daughter from execution. Singh curtly replied he would, much to Pierce's amusement. When Pierce prepared to shoot him, Councilwoman Hawley suddenly attacked Pierce and his men, single-handedly taking them all down. She then held a shocked Pierce at gunpoint, and revealed herself to be none other than Black Widow in disguise. While this was happening, Rogers and Wilson managed to replace the targeting blades on two of the three Helicarriers. However, on the third carrier, Rogers and Wilson were attacked by the Winter Soldier. Wilson was thrown off the ship and managed to parachute to safety on top of the Triskelion, but his suit was damaged beyond repair. Rogers, however, remained on the ship and headed for the control room. In the Council chamber, Romanoff began to disable the security protecting classified information, and proceeded to dump it on the Internet, exposing HYDRA's infiltration to the world. Pierce pointed out that it would also expose S.H.I.E.L.D.'s and Romanoff's dirty business in the process, but Romanoff was undeterred. Pierce then realized that such a declassification of information required two Alpha-level members of S.H.I.E.L.D. for authorization. Just then, Nick Fury arrived by helicopter and confronted Pierce. Pierce attempted to convince Fury that their ambitions were the same, but Fury refused to listen and forced Pierce to deactivate the security along with him. Rogers then confronted Barnes in the control room. After attempting to persuade Barnes to relent, Rogers then engaged him in brutal hand-to-hand combat. The two battled back and forth until finally Rogers broke Barnes' shoulder and partially suffocated him. However, while he attempted to replace the chips in the system, Barnes shot him from below. Pierce then used his phone to activate the white phosphorus-laced biometric identification tags the Council members were wearing, burning through their flesh and severely damaging their internal organs to the point of death. Romanoff, having disguised herself as Hawley, was forced to drop her gun due to the tag on her chest. When the Helicarriers reached 3000 feet above mean sea level, they synced to their targeting satellites in orbit. They acquired thousands of targets, employing Zola's algorithm to find and track them. Just as the ships' long-range precision guns were ready to fire, a wounded Rogers replaced the last targeting blade, disabling the control systems in the carriers. This allowed Agent Hill to take remote control of the Helicarriers, promptly redirecting the ships to fire on each other. The Helicarriers began to destroy each other, with Rogers and Barnes still trapped on one of them. A disappointed Pierce then intended to make his escape, using Romanoff as a hostage to ensure his getaway flight would proceed safely. However, Romanoff activated a Taser Disk in her hand, which sent a current through her body and disabled the tag on her chest. Romanoff collapsed to the floor, and as Pierce tried to reactivate the tag, Fury picked up a gun and shot Pierce dead. With Rumlow heading for the Council room, Hill ordered Falcon to head him off. The two engaged in hand-to-hand combat following an ambush by Falcon, but their fight was interrupted by one of the falling Helicarriers crashing into the building. Rumlow was buried under the cascade of rubble, but Falcon threw himself through a window and landed in a helicopter piloted by Fury. In the falling Helicarrier, Rogers removed Barnes from fallen rubble, and attempted to convince Barnes of his identity. A confused and infuriated Barnes assaulted Rogers, but suddenly remembered that they were friends when Rogers repeated one of the catchphrases that defined their relationship. Rogers fell from the Helicarrrier as debris collapsed the floor out from under him, although Barnes did not. Rogers landed in the but was saved from drowning by Barnes, who helped him ashore and vanished from sight. Rogers was later hospitalized, along with Rumlow.

Aftermath
Because of information Black Widow shared across the internet, S.H.I.E.L.D. was labelled a terrorist organization and the international community disavowed any cooperation with it. Congressional hearings were held with the purpose of questioning various S.H.I.E.L.D. agents, including Romanoff and Hill. Both managed to avoid imprisonment, with Romanoff declaring that they needed her, and could not afford to lock her up. To this the hearing committee had no answer, and Romanoff was allowed to leave. Maria Hill managed to obtain a job at Stark Industries, although she was still pursued by the FBI. Nick Fury, meanwhile, continued to live on in secret, with the world still believing him to be dead.

The Winter Soldier went to the Smithsonian Institution where he observed the Howling Commandos display, reflecting on and absorbing information that HYDRA had attempted to purge from his memory.

The Hub became one of S.H.I.E.L.D.'s main headquarters in the aftermath of the failed HYDRA takeover attempt there.

HYDRA operatives throughout S.H.I.E.L.D. were tasked with purging all S.H.I.E.L.D. facilities of non-HYDRA personal while S.H.I.E.L.D. agents fought back against HYDRA. Eventually two factions of S.H.I.E.L.D. rose up. One was lead by Phil Coulson and the other was lead by Robert Gonzales. The building of the two different factions led to a S.H.I.E.L.D. Civil War. Many S.H.I.E.L.D. agents, suddenly out of work, sought jobs in other parts of the intelligence community, such as Sharon Carter, who joined the CIA.

The civilian community partially blamed President Matthew Ellis for the debacle. Eventually, President Ellis commissioned the creation of the Advanced Threat Containment Unit, as the previous organization tasked with public protection against extraterrestrial threats ended up causing damage to Washington, D.C. and threatened the United States as a whole.