The Capture of Arnim Zola was an operation organized by the Strategic Scientific Reserve and conducted by the Howling Commandos, in order to track down and abduct Arnim Zola who had the key information about HYDRA's plans.
- "We are close to an offensive network that will shake the planet, and yet we are continually delayed, because you cannot outwit a simpleton with a shield!"
"This is hardly my area of expertise. I... I merely develop weapons. I... I cannot fire them."
"Finish your mission, Doctor. Before the American finishes his."
- ―Red Skull and Arnim Zola
In early 1945, the Strategic Scientific Reserve had managed to crack HYDRA's encryption codes and were able to listen in on their radio communications. This ability, coupled with other intelligence, allowed the SSR to confirm Arnim Zola's presence on board a Schnellzug EB912 traveling through the Central Eastern Alps along the Danube River. The Howling Commandos, led by Captain America, were assembled and tasked with the recovery of Zola.
Hijacking the Train
Having calculated where the armored train would be, the Howling Commandos posted up on a nearby cliff overlooking the tracks as Gabe Jones confirmed that Zola was a passenger. The Commandos set up a zip-line from the cliff to the mountainside on which the tracks ran, allowing them to travel safely over a deep valley. One by one, Captain America, Bucky Barnes, and Jones slid over the valley and landed on top of the train as it passed by, with Jacques Dernier calling out when each member of the assault team should begin their jump. The other Howling Commandos stayed behind, acting as overwatch for the now-in-progress mission.
When the three assaulters landed on the top of the train, they began to carefully walk to where they were supposed to go: Rogers and Barnes worked together as a distraction/infiltration team, inserting near the middle of the train, to draw Zola's guards away from him; while Jones continued walking along the top to reach Zola.
The plan began as it should have, as swarms of HYDRA guards began pouring out of the pilot and into the middle cars of the train. Barnes and Rogers engaged them in a tense firefight, trading shots from behind cover. Unfortunately, the duo was separated by mechanical doors as their enemies emerged. Rogers managed to kill his one assailant; a soldier wielding HYDRA Cannons, and used it to blast open the first of the doors, allowing him to manually open the second. Rogers tossed an M1911 pistol to Barnes, who had run dry of ammunition, and the two worked in tandem to kill the remaining HYDRA guard in the room.
Before the pair could celebrate, another HYDRA soldier attacked Captain America and Bucky Barnes, again wielding the HYDRA Cannons. Rogers pushed Barnes out of the way and deflected an energy pulse. The blast ripped the side of the train open, exposing the interior to the cold winter air outside as Rogers was knocked on his back from the force.
Seeing that the HYDRA soldier was charging up another shot, Barnes leaped to his feet and scooped up Captain America's Shield, and shot at the guard. Unfortunately, Barnes was unable to kill his enemy, who fired another pulse of energy. This blast sent Barnes flying out of the train, though he was able to grab part of the destroyed hull and hang on. Rogers recovered from his own stumble and quickly killed the HYDRA guard before rushing out to try to save his friend. As Rogers urged Barnes to take his hand, the railing Barnes was clinging to snapped, sending him plummeting into the icy river in the valley below. Rogers could only look on in horror, shock, guilt, and regret as his friend fell.
As Arnim Zola had been radioing his troops directly, urging them to kill Steve Rogers and Bucky Barnes, he was not focused on keeping himself safe. As such, he did not hear Gabe Jones' footsteps on the roof, and was taken by surprise when he burst through the ceiling window, Thompson submachine gun in hand and held Zola and the HYDRA conductor at gunpoint. Jones arrested the pair, and the Howling Commandos, with the exception of Barnes, were eventually extracted.
Arnim Zola was brought to a Strategic Scientific Reserve prison, where he was interrogated by Chester Phillips on Johann Schmidt's endgame. Phillips noted that Zola had not committed suicide via cyanide pills as the other captured HYDRA agents had. While Phillips suspected that Zola merely wanted to live; Zola, in fact, was planning to rebuild HYDRA inside the United States Government; believing that Schmidt had become delusional.
Eventually, the information Zola provided, coupled with other intelligence gathered by the SSR led to the final assault on HYDRA; the disappearance of Captain America; and the ultimate collapse of HYDRA in Europe. While imprisoned, Zola gained Johann Fennhoff as a cellmate and asked him about the nature of his mind control powers.
The New HYDRA
Arnim Zola's capture also provided one of the earliest examples of recruitment to Operation Paperclip, and as such, provided the framework for rebuilding HYDRA inside S.H.I.E.L.D. and the United States Government.
Unbeknownst to anyone, Bucky Barnes, in fact, survived his fall, due to Zola's experiments at the Austrian HYDRA Weapons Facility. He was captured by Soviet Armed Forces and taken to Zola who personally forged him into HYDRA's assassin, known as the Winter Soldier. All Barnes' memories about his entire life before HYDRA, wiped, and he would be reprogrammed to assassinate those whom HYDRA believed could pose problems for its plans of world domination. Kept in a Cryostasis Chamber between missions, he would go on to shape the twentieth century.