The Battle of the HYDRA Siberian Facility was an open confrontation that pitted Captain America and the Winter Soldier against Iron Man.
Helmut Zemo located Vasily Karpov, one of the former leaders of the Winter Soldier Program, who was in hiding with HYDRA having been wiped out. Having discovered Karpov's location, Zemo knew that he would be unable to easily break into Karpov's home so instead faked a car crash and asked Karpov to invite him inside to discuss the matter in private.
As soon as Karpov opened the door, Zemo attacked and subdued Karpov before tying him upside down above a sink slowly filling with water. Using a hammer to bust through the walls of Karpov's cellar, Zemo found and took the Winter Soldier Book from Karpov's HYDRA files and introduced himself while speaking politely to Karpov, before demanding information that occurred back in the year 1991.
Despite Zemo making his intentions very clear that he would not stop until he had the information he needed to exact his violent revenge, noting that his loyalties did not lie within HYDRA, Karpov refused to help him. Seeing that Karpov would not speak to him, Zemo left the tap running while Karpov gave the famous HYDRA salute.
Zemo then walked straight out of the house, taking his new stolen belongings. Bucky Barnes had been framed for a bombing attack on the Vienna International Centre the day the Sokovia Accords were being signed.
Barnes' friend Steve Rogers brought it on himself to bring Barnes in, knowing that ordinary humans would not survive an encounter with a super soldier, especially one that had once nearly beat him to death. However, Barnes tells Rogers that he does not do assassinations anymore and that the attack in Vienna was not his.
A chase through Bucharest only resulted in Barnes, Captain America, Sam Wilson and T'Challa being arrested. All four were escorted to a Joint Counter Terrorist Centre Building. The two Avengers and T'Challa were placed in an office and had their equipment confiscated, while Barnes was heavily restrained in a mobile cell, to be psychologically evaluated.
Prior to Barnes' interrogation, Theo Broussard, the psychiatrist who was supposed to be carrying out the evaluation, was murdered by Helmut Zemo, the true perpetrator of the Vienna bombing. Zemo impersonated Broussard, and carried out the evaluation as normal until he was able to speak a trigger phrase intended to activate Barnes' Winter Soldier programming and send Barnes on a rampage.
Captain America realised that Broussard was an impostor, but was too late to prevent the attack. After killing several Joint Counter Terrorist Centre employees and nearly killing Black Widow, Barnes attempted to escape in a helicopter, but Captain America prevented him from leaving, causing Barnes to crash it. Captain America saved Barnes from drowning after falling into the river, and Barnes' Winter Soldier programming had worn off by the time he awoke.
The Joint Counter Terrorist Centre gave Iron Man 36 hours to capture Barnes and bring in his renegade comrades. Although James Rhodes, Vision, Natasha Romanoff and Black Panther agreed to help Stark, he still felt undermanned and recruited high school student Peter Parker, who Stark had managed to discover was a superhero named Spider-Man, under the pretense of giving him a educational grant under the Stark September Foundation program.
After enlisting Clint Barton to rescue Wanda Maximoff and recruit Scott Lang, who had been recommended by Wilson, Rogers and his team made their way to Flughafen Leipzig-Halle, where a Quinjet was waiting to take them to Siberia.
Iron Man evacuated the airport, alerting Captain America and his team to the heroes' presence. Captain America jogged out onto the runway towards a helicopter, which was then quickly disabled by Iron Man as he, War Machine, Black Panther and Black Widow approached Captain America. Captain America attempted to convince them that Barnes was innocent, however Iron Man grew impatient and ordered Spider-Man to web Captain America's hands and steal his shield.
Falcon soon located the Quinjet and notified Captain America, who then gave the signal to Hawkeye. Hawkeye fired an arrow at the webbing, freeing Captain America as Ant-Man revealed himself to be hiding on Captain America's shield and managed to take Spider-Man by surprise, hitting him and retaking the shield.
Stark turned around to the source of the arrow, locating Hawkeye and Scarlet Witch via scan as War Machine announced Falcon and Barnes' position and the battle began.
Following the Clash, Barton, Lang, Maximoff, and Wilson were captured and imprisoned in the Raft while Parker was sent back to New York by Stark's request.