The War on HYDRA was a conflict between the terrorist organization HYDRA and the Avengers, S.H.I.E.L.D., and the United States of America after the revelation of HYDRA's continued existence within S.H.I.E.L.D.. At first, HYDRA had the upper hand over S.H.I.E.L.D. because S.H.I.E.L.D. was reduced to only a shadow of its former strength, and the HYDRA leader Daniel Whitehall used that to retrieve the mysterious Obelisk. However, once S.H.I.E.L.D. was redeemed in the eyes of the law, they turned the tables on HYDRA, who lost the battle for the ancient Kree City, and many of its leaders, including Whitehall, in rapid succession. Though Baron von Strucker and Doctor List continued HYDRA's experiments on enhanced people, their efforts were rendered null when their HYDRA cell was destroyed by S.H.I.E.L.D. and the Avengers – only a year after their uprising, HYDRA was on the brink of ruin. After Baron von Strucker's death at the hands of Ultron, only a few scattered HYDRA cells remained operational, and each of their leaders, Mitchell Carson, Hale, Gideon Malick, and Grant Ward, tried to rebuild the organization in their own way.
- "The corrupt institution has been dismantled, yes. We cut down the tree, we pulled up the roots, but let's just say I'll rest easier when we put them all on the bonfire."
- ―Glenn Talbot
HYDRA revealed itself to the public as an active organization despite its apparent defeat following the end of World War II. Despite its collapse, S.H.I.E.L.D. was secretly reformed  and the Avengers were officially reassembled to fight HYDRA.
However, HYDRA was still incredibly strong. In the eyes of the law, S.H.I.E.L.D. was still a terrorist organization, and the United States Armed Forces were hunting both S.H.I.E.L.D. agents and HYDRA operatives.
Daniel Whitehall's Campaign
With S.H.I.E.L.D. being outlawed and reduced to just a few dozen agents, HYDRA could do much more on spreading its influence and accomplishing its plans for world domination. A few months after the Battle at the Triskelion, the HYDRA leader Daniel Whitehall resumed his search for the Obelisk, which he first discovered at the end of World War II, when he was still known as Werner Reinhardt. After the fall of S.H.I.E.L.D., the Obelisk was confiscated by the United States Armed Forces, and Whitehall's second in command, Sunil Bakshi, hired the enhanced criminal Carl Creel to steal it. At first, Creel's mission was successful, but the Obelisk was stolen from Bakshi and Creel was captured by S.H.I.E.L.D. and turned over to General Glenn Talbot.
Daniel Whitehall's HYDRA planned to capture Donnie Gill in order to use him for their needs. Gill discovered it and froze the ship that was meant to take him, the Maribel del Mar, therefore alerting both HYDRA and S.H.I.E.L.D.. Sunil Bakshi took with him Jemma Simmons, the undercover S.H.I.E.L.D. agent to persuade Gill to join HYDRA. Phil Coulson got the information from Alphonso Mackenzie that HYDRA planned to brainwash Gill. Lance Hunter was about to shot Simmons, who recited the brainwashing lines from Bakshi, but Melinda May saved her by shooting and Hunter. Gill got mad, so Bakshi tried to brainwash him again and succeed. Skye could not let HYDRA taking Gill, so she shot him to death. HYDRA escaped and S.H.I.E.L.D. got their hands on HYDRA equipment.
HYDRA managed to weaponize the Obelisk. Whitehall decided to test it at the wedding of Pete Leitner and Mariah against the anti-HYDRA unit of United States Armed Forces. The wedding was attended by many of Peter's colleagues from the Navy. The wait staff started to serve champagne to the guests and would not allow them any other drink. The guests who drank the champagne started to petrify and died. Some of the wedding guests suffered no effects while others had to be hospitalized.
Two days later, Simmons had her cover blown due to Raina sending an email to every HYDRA operative at the HYDRA Laboratories, with a photo of Simmons using the Flex Screen that incriminated Kenneth Turgeon. Bakshi ordered his men to grab Simmons, but she escaped the room, coming across Bobbi Morse, head of security at the Laboratories. Simmons thought she was done, but Morse attacked her escort, revealing her identity as a fellow undercover S.H.I.E.L.D. agent. Morse instructed Simmons to wait while she got rid of some guards, but Simmons witnessed Bakshi approaching her position. Both Simmons and Morse ran to the roof where, following a brief shootout between Morse and the HYDRA operatives pursuing them, both agents jumped off the roof onto a cloaked Quinjet piloted by Antoine Triplett. 
Redemption of S.H.I.E.L.D.
Daniel Whitehall ordered Marcus Scarlotti and his team to impersonate S.H.I.E.L.D. agents and use Splinter Bombs to attack a United Nations meeting to turn the world further against S.H.I.E.L.D. Ironically, this made Glenn Talbot, who had traditionally treated HYDRA and S.H.I.E.L.D. as one and the same, doubt his original position. Senator Christian Ward was afraid of criticism for his failure to destroy S.H.I.E.L.D. in an election period. He publicly criticized the organization, and proposed international attempts to destroy it. Phil Coulson quickly took action and offered to hand him his brother Grant Ward so he could look like a hero for putting his own brother on trial. In exchange, he wanted the senator to publicly reverse his proposal, to condemn HYDRA, treat it as separate, and to vindicate S.H.I.E.L.D. The senator agreed and this also led to Talbot finally coming to respect S.H.I.E.L.D. and to cease trying to arrest its members. Talbot even arrested Scarlotti and his team as well as Julien Beckers, after which he respectfully shook hands with Melinda May and lamented the loss of her brave agents. S.H.I.E.L.D. was finally safe from persecution and the tables had been turned against HYDRA. This also made it easier for Coulson to recruit new agents, even though S.H.I.E.L.D. largely continued in the shadows.
Race to the City
Phil Coulson discovered the Words of Creation were a map of a city. Meanwhile, Grant Ward and Calvin Zabo joined Daniel Whitehall's HYDRA, whit Zabo telling him the origin of the Obelisk, or the Diviner, was Kree.
To find the city, Coulson's team arrived at Laura Creek Station, they were attacked by HYDRA soldiers. Leo Fitz untied the station's crew and locked them in a secure room. Fitz began the hack and Antoine Triplett covered his back as two soldiers entered. Triplett killed the first but was shot in the shoulder by the second soldier before he was shot by Coulson. As they tried to help Triplett, Zabo arrived and offered his help, telling them that he was a doctor.
As Zabo seemingly performed first aid, he actually slit Triplett's artery, using his life as blackmail, because it would allow him time to escape the scene while Coulson and Fitz helped Triplett after their conversation about Skye was finished. When he had gotten what he wanted, he gave them a clotting agent to save Triplett from bleeding to death. Zabo escaped from the station. Fitz finished the hack and helped Coulson get Triplett back to the Bus.
The next day, Raina and her boyfriend Chad were in a coffee shop in Vancouver. Raina spotted Melinda May and approached her but it was actually Agent 33, who told her Daniel Whitehall would like to speak to her. Raina ran out the door and down the street. She passed Agent Billy Koenig who told her to take a right at the corner where his brother Sam Koenig was waiting. Sam told Raina to come close to him and used a Cloaking Umbrella to conceal them from HYDRA agents.
The Koenigs took Raina to a S.H.I.E.L.D. Safe House and contacted Phil Coulson, who sent May, Skye and Lance Hunter to extract them. May and Hunter took out several HYDRA agents searching the area and Skye headed to the safe house to collect Raina. As they were leaving, Agent 33 attacked Skye. Skye ordered Billy Koenig to take Raina and head for the stairs while she engaged Agent 33. Skye disarmed her and threw her through the door of the safe house. Skye restrained Agent 33 and offered to help her but Agent 33 broke free, knocked Skye to the ground and grabbed her gun. She took aim at Skye but was tackled to the ground and knocked out by Hunter. However, when Raina found out that Whitehall had the Diviner, she tried to hand herself over to HYDRA, but the rest of Coulson's team prevented her, and they all returned to the Bus.
Phil Coulson and Bobbi Morse entered San Juan, and met up with Morse's tour guide contact Diego, who gave them plans to the Castillo San Cristóbal. When they entered the garrison, they called in Leo Fitz, Jemma Simmons and Alphonso Mackenzie to come to the site as they realized the city was underground. Mackenzie used the Mouse Hole to cut a hole in the floor and Fitz sent his D.W.A.R.F.s down a tunnel to find out what was down there, but the controls failed. Since technological methods did not seem to work, Mackenzie volunteered to descend into the city to see it for himself, but when he touched a Kree symbol on the floor, he lost control of his body.
When the team brought him back up, he attacked them all ruthlessly with no sign of his normal personality inside as an end result of the painful transformation he went through mentally and physiologically. Coulson tried to shoot him, but he seemed to be immune to I.C.E.R. bullets, and was only defeated when Morse electrocuted him with her staves and he fell down the tunnel. It was unclear to the team whether or not he survived the drop.
Agent 33 reported to Daniel Whitehall that Raina mentioned S.H.I.E.L.D. implanted her with a tracker. Grant Ward recognized the old S.H.I.E.L.D. frequency, tracked the Bus, and led HYDRA to the plane until they had it surrounded by Quinjets. Ward boarded the Bus and promised not to attack so long as he can take Skye and Raina with him. Reluctantly, S.H.I.E.L.D. handed over them over, along with the maps of the city, evening the odds between S.H.I.E.L.D and HYDRA, since both sides now knew the location of the Kree City.
Whitehall received the news that Ward did not destroy the Bus, and ordered the strike team to do it himself. Agent Melinda May was suspicious of their intentions, and ran directly to the cockpit. She used multiple maneuvers to lead them down into cloud cover, and released countermeasures as they went into cloaking mode to escape the HYDRA Quinjets. The jets registered the attack as successful, believing they had hit the Bus with four direct hits. However, May tricked them and flew to Coulson. Coulson prepared his agents for the Battle for the Kree City. Meanwhile, he gave the Koenig brothers orders to have Theta Protocol ready if HYDRA won.
May landed the Quinjet atop the theater. The four agents of S.H.I.E.L.D. entered, guns blazing. Whitehall heard the gunshots. He and Agent 33 went to investigate, leaving Skye and Grant Ward tied in chairs and Calvin Zabo paralyzed on the floor. HYDRA operatives went up the stairs while S.H.I.E.L.D. agents came down. Ward distracted the guard long enough for Zabo to remove the paralyzing device on his neck and kill the guard. Zabo refused to free Ward and Skye because he did not want them to see him kill Whitehall. Ward freed himself and then freed Skye. She took the guard's gun and shot Ward to pursue her father. The Bulletproof Vest he wore saved his life.
Zabo and Whitehall saw one another near a staircase. Zabo smiled as he approached his wife's killer; Whitehall drew his weapon to eliminate a man whose worth to him had ended. However, Whitehall was killed ignominiously by Phil Coulson. When Calvin Zabo saw that his planned revenge would not happen, he angrily shouted at Coulson until Agent 33 shot at them, chasing them away. Skye found the two struggling. As Zabo began beating Coulson to death, Skye stopped him at gunpoint and ordered him never to see her again. Zabo promised that she would come to him after she transformed because only he would understand.
The Crippling Blow
With Daniel Whitehall killed and Sunil Bakshi in S.H.I.E.L.D.'s custody, HYDRA felt vulnerable. List offered Whitehall's position to whoever could destroy S.H.I.E.L.D. Meanwhile, Phil Coulson offered Bakshi to Glenn Talbot, who was supportive of Coulson now. He offered to hand over Bakshi in exchange for further help to fight remaining HYDRA forces. First, however, Coulson planned to use Bakshi to further destroy HYDRA. With the help of his deputy Melinda May and various agents he staged a HYDRA attack where it looked like both he and May got killed. Lance Hunter pretended to work for HYDRA and helped Bakshi escape, allowing him to call Octavian Bloom. After he made the call, Hunter pretended to be paid by multiple members of HYDRA to take both Bakshi and Bloom out. Bakshi offered an enormous amount of money if Hunter took him to Bloom. Once at Bloom's protected mansion he told Hunter to stay in the car. He went to Bloom and told him of what happened and they contacted List. They informed him that the Banker, the Baroness, and the Sheikh were conspiring against them. They contacted HYDRA members to have all three assassinated. Bakshi also sent six HYDRA agents to kill Hunter.
Meanwhile, Bobbi Morse got in the car with Hunter. The car was bullet proof however, and revealed secret guns that killed all the agents. Then the car crashed through the gate and Morse and Hunter went into the mansion, killing both guards, surrounding Bloom and killing him. They took Bakshi into their custody again to deliver him to Talbot.
The Final Battles
HYDRA scientist Doctor List was researching a phenomenon called Quantum Entanglement; it occurred any time the Inhuman Gordon would use his teleportation power. List would capture people who were in the vicinity of the Entanglement, and experiment on them, but he was unable to find its originator. Gordon teleported Skye and Calvin Zabo to Milwaukee; List traced the Entanglement to Calvin Zabo's Building.
Phil Coulson was in pursuit of Doctor List; he recruited Deathlok to apprehend him. To get closer to HYDRA, Coulson recruited Grant Ward, who had Kara Palamas accompany him. The group created a plan to use the thralled Sunil Bakshi to infiltrate HYDRA, get close to List, and set up List's capture. They followed him to Calvin Zabo's building.
Bakshi, Deathlok and a team of HYDRA agents arrived and attacked. The Inhuman Lincoln Campbell used his electrical powers to subdue the first agent and Zabo killed three more. Campbell ordered Skye to run as her powers could destroy the building. Deathlok spotted Skye but Campbell used his powers to lift him off the ground but he was unable to hold him for long due to his cybernetic implants. Coulson, Ward, Lance Hunter, Leo Fitz and Agent 33 landed on the roof in a Quinjet and headed into the building. Coulson and Ward headed to find Skye while Hunter and Agent 33 engaged the HYDRA agents. Hunter was shot in the side by one of the agents before he was killed by Agent 33. Coulson and Ward came upon Deathlok and Campbell, who were still fighting. Deathlok scanned for Skye and Coulson and Ward headed in her direction as Bakshi entered the hall with two agents. Bakshi ordered the agents to take them both and one fired a Pulse Grenade that knocked them both out.
Coulson and Ward found Skye but Gordon appeared to teleport Skye back to Afterlife. Zabo entered the teleportation field and was transported as well. A HYDRA agent took aim at Coulson but was shot in the back by Ward. With Hunter injured and HYDRA outnumbering them, Coulson ordered his team to evacuate while he stayed behind and surrendered to Bobbi Morse and Alphonso Mackenzie.
Coulson made a deal with Robert Gonzales in hopes to reunify S.H.I.E.L.D. against HYDRA and to end the S.H.I.E.L.D. Civil War. The reunified S.H.I.E.L.D. mounted the Attack on the Arctic HYDRA Research Facility to rescue Campbell and Deathlok. Coulson's team for the mission consisted of all the members of his old team: Grant Ward, Melinda May, Jemma Simmons, Leo Fitz and Skye. The mission had two teams; Skye, Ward and Simmons were rescue/medical, and the other team was Coulson and Fitz, who would break into the missile defenses and gather intelligence, while May would provide cover.
Doctor List and Sunil Bakshi were chatting about the prisoners' progress when a HYDRA operative entered and told them that they detected a plane. Bakshi realized it was S.H.I.E.L.D. so List ordered the operatives to shoot them from the sky. HYDRA then shot missiles at the Bus, destroying it. Coulson's team managed to escape the damage in a Quinjet.
They then broke into the base. When they got inside, they found Bakshi, who took down some guards. Bakshi asked Coulson if he could join Ward's team; Coulson agreed. Coulson then told everyone that they had only fifteen minutes before Robert Gonzales' jets arrived. Once Ward's team broke into the lab, the HYDRA operatives took List away. Skye then used her powers to take down the remaining operatives in the room. Jemma Simmons and Skye found Deathlok; Skye asked him where Lincoln Campbell was and he said he was in the other room but she had to hurry because he was in pretty bad shape. Skye took down the remaining operatives in the lab to rescue Campbell. When she reached Campbell, he was dead; she used her powers to start his heart again, saving his life.
While Grant Ward was looking for something to use to carry Deathlok, Simmons arrived from behind a wall carrying a Splinter Bomb. She went to throw when Bakshi stepped in the way. The bomb activated on his chest, disintegrating him. Meanwhile, Coulson and his team took down the operatives in the mainframe room. Leo Fitz then started hacking into the system to disarm the missiles. Fitz was almost done disarming the missiles when Melinda May noticed Coulson was missing. She then found Coulson in another room on a computer gathering intelligence. She shot two operatives who were approaching and told him he was next if he did not come. May then contacted the Playground and told them they had the prisoners and were leaving HYDRA air space. Gonzales then ordered the jets to fire at the base.
Using information provided by Phil Coulson during the Attack on the Arctic HYDRA Research Facility, Maria Hill helped the Avengers locate Strucker's base and launch an assault. Upon arriving in Sokovia, the Avengers carried out their plan, unaware that Wolfgang von Strucker had learned of their presence and alerted his men. Black Widow and Hawkeye drove through the forest in a stolen Jeep, the latter neutralizing several HYDRA soldiers with his trick arrows. As the team converged on the perimeter, Black Widow crashed the Jeep and jumped out with Hawkeye before helping Captain America, Thor and Hulk fight off incoming soldiers. Iron Man attempted to enter the compound only to be repelled by an energy shield. J.A.R.V.I.S. analyzed the shield and mentioned that Strucker's technology was more advanced than the other bases they had raided.
Inside the compound, Strucker deployed the tanks as List proposed that they send Pietro and Wanda Maximoff as a distraction. Strucker refused, confident that his men were capable of emerging victorious. Meanwhile, J.A.R.V.I.S. alerted Iron Man that the troops were firing on Novi Grad. The latter then sent the Iron Legion to evacuate the area. Despite some resistance, the Legion successfully managed to get several civilians to safety. Inside the base, Strucker rallied his men with a speech before privately telling List that he planned to surrender and carefully instructing the scientist to erase all data from the base's computers. Before List could take any action, however, the two realized the twins were missing.
Meanwhile, in the woods, Hawkeye was preparing to destroy a bunker with an explosive arrow when he was distracted by Pietro, who used his supersonic speed to distract the former S.H.I.E.L.D. agent before taking off. Hawkeye prepared to aim his bow at Pietro, but was shot in the side by one of the bunker's turrets and gravely wounded. Romanoff came to his aid while the Hulk destroyed the bunker. Pietro then attacked Captain America before making his way back to the base. Captain America relayed the information to Stark and followed Pietro as Thor helped Black Widow get Hawkeye to the Quinjet.
Having located a power source in the compound's northern section, Stark destroyed it and deactivated the energy shield. After neutralizing several HYDRA soldiers, Stark found Doctor List, who was erasing his files. After fatally shooting List with a repulsor ray, Stark placed his armor in automated sentry mode before tasking J.A.R.V.I.S. with copying the remaining files and sending them to Avengers Tower. In the forest, the HYDRA soldiers surrendered and were taken into custody as Romanoff approached Hulk and recited a lullaby that helped him calm down and transform back into Bruce Banner.
While Stark discovered a secret passage, Rogers confronted Strucker about his experiments only to be attacked by Wanda, who quickly fled the scene. Rogers subdued Strucker and informed the others. Meanwhile, Stark continued following the secret passage and entered an underground laboratory housing Chitauri armor and weaponry as well as a Leviathan corpse. He found the Scepter and moved forward to take it from its resting place. Before he could do so, however, Wanda crept up behind him and used her powers to implant a vision into his mind. Sensing Wanda's presence, Stark turned around to find that he was alone. Suddenly, the Leviathan corpse came to life as Stark found himself in Chitauri Space, surrounded by his teammates' lifeless bodies and forced to watch the Chitauri invade Earth. Snapping out of his trance, Stark summoned one of his armor gauntlets and took the Scepter as Wanda and Pietro watched from the shadows.
The terrorist organization suffered major setbacks following the defeat of Wolfgang von Strucker by the Avengers. Strucker was one of the last remaining leaders of HYDRA, and much of their equipment and weaponry was either taken away or were used by Ultron in his own war against the Avengers.
Only a few scattered HYDRA cells remained operational. One of them, led by Mitchell Carson, managed to obtain the Pym Particle technology. Another cell was taken over by Grant Ward, who appointed himself as its new leader with the intention to rebuild the organization and destroy Phil Coulson and S.H.I.E.L.D. Werner von Strucker, the son of Wolfgang von Strucker, was recruited by Ward and planted in the psychology class of consultant Andrew Garner, ex-husband of Agent Melinda May.
With S.H.I.E.L.D. under Phil Coulson focusing so much attention on HYDRA and its own internal strife, the United States President Matthew Ellis authorized the Advanced Threat Containment Unit to find newly-powered individuals and aliens for containment and study, a job once done by S.H.I.E.L.D. However, the ATCU was infiltrated by a third cell of HYDRA led by Gideon Malick, who had been able to keep his cover within the government the whole time, and using the ATCU, this cell was able to build an army of Inhumans for Malick's master plan to accomplish HYDRA's longest goal.
Eventually, Malick's cell and Ward's cell interacted, and after a brief struggle, the two joined forces to accomplish their goals. At the same time, S.H.I.E.L.D. and the ATCU's leader, Rosalind Price discovered the HYDRA infiltration within her organization, and figured out that they were behind recently discovered secret elements of the ATCU. Learning of Coulson's affection with Price, Ward assassinated her as she was having dinner with Coulson and discussing how best to deal with the HYDRA infiltrators in her organization. This action would lead to another large-scale confrontation between S.H.I.E.L.D. and HYDRA.
- ↑ Agents of S.H.I.E.L.D.: 2.12: Who You Really Are
- ↑ 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 (2012)
- ↑ Agents of S.H.I.E.L.D.: 2.01: Shadows
- ↑ Captain America: The Winter Soldier
- ↑ Agents of S.H.I.E.L.D.: 1.22: Beginning of the End
- ↑ Avengers: Operation HYDRA
- ↑ Agents of S.H.I.E.L.D.: 2.01: Shadows
- ↑ Agents of S.H.I.E.L.D.: 2.02: Heavy is the Head
- ↑ Agents of S.H.I.E.L.D.: 2.03: Making Friends and Influencing People
- ↑ Agents of S.H.I.E.L.D.: 2.05: A Hen in the Wolf House
- ↑ Agents of S.H.I.E.L.D.: 2.06: A Fractured House
- ↑ Agents of S.H.I.E.L.D.: 2.07: The Writings on the Wall
- ↑ Agents of S.H.I.E.L.D.: 2.08: The Things We Bury
- ↑ 16.0 16.1 16.2 Agents of S.H.I.E.L.D.: 2.09: ...Ye Who Enter Here
- ↑ Agents of S.H.I.E.L.D.: 2.10: What They Become
- ↑ Agents of S.H.I.E.L.D.: 2.11: Aftershocks
- ↑ Agents of S.H.I.E.L.D.: 2.18: The Frenemy of My Enemy
- ↑ Agents of S.H.I.E.L.D.: 2.19: The Dirty Half Dozen
- ↑ 21.0 21.1 Avengers: Age of Ultron
- ↑ Ant-Man
- ↑ Agents of S.H.I.E.L.D.: 2.22: S.O.S. Part Two
- ↑ Agents of S.H.I.E.L.D.: 3.02: Purpose in the Machine
- ↑ Agents of S.H.I.E.L.D.: 3.01: Laws of Nature
- ↑ 26.0 26.1 Agents of S.H.I.E.L.D.: 3.08: Many Heads, One Tale
- ↑ Agents of S.H.I.E.L.D.: 3.09: Closure