War on HYDRA

"We cut off the head. And while HYDRA scrambles for a new one, I will crush them! I'm gonna make somebody pay whoever the hell it is."

- Phil Coulson

The War on HYDRA was a conflict between the terrorist organization HYDRA and all world governments and security organizations after the revelation of HYDRA's continued existence. 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, the remaining fragments of HYDRA were taken over by Grant Ward.

Background
"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
"Creel has escaped and did indeed make off with the Obelisk. He should contact us shortly. I would have him come in, but I'm being overly discreet with this operation. I know how long you have been searching for this, Dr. Whitehall." "You have no idea."

- Sunil Bakshi and Daniel Whitehall

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.

Undercover Mission
To be added

Redemption of S.H.I.E.L.D.
"But as is so often true, the darkness lingers longer than the light. And while S.H.I.E.L.D. is gone, HYDRA is a problem that world must still face. Otherwise, that darkness will grow and spread and cast a shadow over us all."

- Christian Ward

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
To be added

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
To be Added

Attack on the HYDRA Research Base
Using information provided by Phil Coulson, Maria Hill helped the Avengers locate Strucker's base and launch an assault, during which the team encountered Pietro and Wanda Maximoff, twins given superhuman abilities by HYDRA. As all of the other Avengers fought HYDRA soldiers both inside and outside of the facility, Tony Stark recaptured the Scepter.

Aftermath
"We don't need to start another war; we just finished one."

- Phil Coulson

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 had by S.H.I.E.L.D. However, the ACTU 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 ACTU, this cell was able to build an army of Inhumans for Malick's master plan to accomplish HYDRA's longest goal.