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The Avengers, who had gone their separate ways after the Chitauri Invasion, regrouped to destroy HYDRA following the revelation that the organization had not been destroyed during World War II and had infiltrated S.H.I.E.L.D.
Hawkeye piloted the Quinjet until the Avengers arrived at the port. When they arrived, the Quinjet was quickly bombarded by HYDRA's explosives. Captain America, Iron Man, Thor and Hawkeye immediately exited the vehicle and attacked the HYDRA soldiers, armed with Chitauri Armor and HYDRA Tanks.
While they attacked, Bruce Banner tried to stay inside the Quinjet until he was needed. Unluckily, HYDRA operatives found him and tried to use their tanks to kill him, only provoking him to transform into Hulk.
The HYDRA operatives realized that they were losing the fight, but Doctor Jensen commanded them to continue fighting. Despite this, they soon fled the port. Without any reinforcements, Jensen chose to use a weapon she had been working on against the Avengers. For a while, Jensen was successful, but Hawkeye shot the weapon's base from behind her, making it explode. Defeated, Jensen lay down in the dirt, puzzled at how she could have possibly lost.
Hawkeye, whose self-confidence was weaning, realized that he was needed on a team that consisted of super-soldiers and gods.
The Avengers were reassembled after a hiatus, knowing that HYDRA was a primary threat. As the War on HYDRA continued, the Avengers were nearby when Maria Hill needed them to wage an Attack on the HYDRA Research Base in Novi Grad, Sokovia.