Civil War is the third Captain America movie, but it could just as easily be the third Avengers movie. Almost the entire MCU comes out for this one in a giant clash of super heroes.
In 1991, at a hidden Hydra base in Siberia, the Winter Soldier is brought out of his frozen hibernation and sent on a mission to recover a mysterious serum.
In the present Captain America is leading a group of the Avengers: Black Widow, Falcon, and Scarlet Witch, on a mission to capture Crossbones, former SHIELD STRIKE leader Brock Rumlow, outed as a Hydra double agent, now working as a mercenary. Crossbones attempts to steal a biological weapon from a viral research center, but the Avengers are able to fight off his men and take back the stolen vials. Faced with capture, Crossbones activates his suicide vest, attempting to blow up himself and Cap, but Wanda is near enough to use her powers to contain the blast and send him flying into the air. Unfortunately she loses control and sends him, flying and exploding, into a nearby building, causing a number of casualties.
Meanwhile, Tony Stark is giving a presentation at MIT, and funding student’s research projects when he is approached by a woman who lost her son in Sokovia. She blames him and the Avengers for her son’s death, and wants to know what they intend to do about it. Elsewhere the commander that sent the Winter Soldier on his mission in ’91 receives a visitor, who insists on learning the details of the mission. When the commander is uncooperative, the visitor kills him and steals the book with the codewords that will activate the Winter Soldier’s mental programming.
Back at the Avenger’s headquarters, Stark, Cap, and the others receive a visit from General Ross, who announces that in light of the growing number of incidents and high casualty rates associated with their operations, particularly after Lagos, the nations of the world have come together to pass the Sokovia Accords, which will require that super powered individuals submit themselves to United Nations oversight if they wish to continue their operations. Feeling his failures in New York and with the Ultron Project, Stark insists that signing is the right thing to do, gaining the agreement of Rhodes and Vision. However, Cap insists that oversight will prevent them from doing what needs to be done, or worse allow them to become tools for organizations like Hydra. Before the conversation can reach any conclusion, Cap is called away by the death of Peggy Carter, and leaves with Falcon to attend her funeral, where he reconnects with Sharon and learns that she was Peggy’s niece.
Black Widow joins the others in the UN building in Vienna for the signing of the accords, and is met by T’Challa of Wakanda, and his father the King. Before the end of the session the UN building is bombed, killing many including the King. Investigations and video evidence pins the bombing on the Winter Soldier. Sharon, now working with the CIA, tips Cap off to Bucky’s possible location, sending him and Falcon off on a race to reach Bucky before the CIA, but Cap is not in time, and ends up trying to help Bucky escape. On the way out they run into T’Challa, as the Black Panther, out seeking revenge against Bucky for his father’s death. A second chase ensues as Black Panther pursues the Winter Soldier, and Cap and Falcon pursue them both, but all four are stopped by War Machine and are arrested and taken back to the UN.
Stripped of their gear, and being held prisoner, Cap is approached again by Stark, insisting that he can smooth the whole mess over if Cap will simply sign the accords and get on board, but Cap again refuses, believing Bucky to be innocent of the bombing and citing the situation as a prime example of why they can’t be under government control. Meanwhile, taking the place of the psychiatrist sent in to interview Bucky, the commander’s visitor, revealing himself to be Helmut Zemo, uses the notebook he stole from the Hydra commander to activate Bucky’s brainwashing and send him rampaging through the building. Stark, T’Challa, Widow, and Cap all attempt to stop him, but Bucky escapes, and in the confusion Cap and Falcon slip out after him, managing to capture him and bring him back to his senses.
Ross declares Captain America and his associates as criminals and demands that they be brought in, giving Stark two days to do so before the military steps in to do it for him. Knowing that Cap won’t come quietly and realizing that his team is highly understaffed he and Widow decide to do some recruitment.
Meanwhile, Bucky tells Cap about Zemo and lets him know that he was asking about the ’91 mission and the base in Siberia. He tells Cap that he is not the only Winter Soldier, and that the serum he stole was used to turn an already effective Hydra death squad into super soldiers, and that they are almost certainly still contained in that base. Realizing that they will have resistance from Iron Man and the government, and expecting a possible fight against the new Winter Soldiers in Siberia, Cap and Falcon decide to do some recruitment of their own to help them reach the Hydra base before Zemo. Sharon is able to return their gear to them, and they set about their mission.
Black Widow approaches T’Challa to secure the Black Panther’s help in the upcoming fight while Stark heads to Queens, surprising high school boy Peter Parker and asking him to come along with him as the hero Spiderman. Hawkeye, after receiving a call from Cap, stops off at Avenger’s headquarters to rescue Wanda who has been being held there under house arrest by Vision at the request of Stark. Despite not wanting to fight Vision, and understanding that he is acting out of concern for her safety, she uses her powers to disable him long enough for her and Hawkeye to escape. They pick up Ant Man on the way to join Cap, Falcon and Bucky in Berlin. As they cross the airport on their way to the quinnjet for their trip they enter a face-off with Iron Man, War Machine, Vision, Black Widow, Black Panther, and Spiderman. The two teams fight, exchanging blows, gaining and losing advantage, as Cap advances toward the jet. When it becomes apparent that they will not all be able to make it, the rest of the team attempts to keep Iron Man’s forces distracted as Cap and Bucky head for the plane. They are able to hold off most of them, but Black Panther and Black Widow follow them to the jet. Widow turns on Black Panther, disabling him and allowing Cap and Falcon to escape. Iron Man and War Machine immediately fly after them, trying to take the plane down, with Falcon trying to take them off the trail. Iron Man calls for the vision to target Falcon’s wings so they can focus on the jet, but distraught over injuries Wanda received in the fight, Vision misses, and accidentally hits War Machine, sending Rhody tumbling out of the sky. The jet gets away as Falcon and Iron Man race to the ground, too late to save Rhody from the fall. The remaining heroes that sided with Cap are captured and taken to the Raft prison, but refuse to give up Cap’s location.
Iron Man receives confirmation that Cap was right about Bucky being manipulated, and pleads with Falcon to let him help, agreeing to go alone and without telling Ross. He catches up to Cap and Bucky as they enter the Hydra base, but they find that the other Winter Soldiers have been killed. Zemo confronts them from a sealed chamber within the base and shows them a retrieved video of the ’91 mission from the Hydra archives, his true purpose in all of this. The video shows the Winter Soldier, not only taking the serum, but killing the people transporting it: Stark’s parents. Enraged that Bucky killed his family, and believing that Cap new about it the whole time, Iron Man attempts to kill Bucky, with Cap fighting back to protect him. Zemo slips out, his work complete, but is met by Black Panther, who followed Tony in secret, and reveals that all of this was to tear the Avengers apart from the inside, as revenge for the death of his family in Sokovia. He attempts to commit suicide, but T’Challa stops him, his own thirst for vengeance dulled by all of the carnage, preferring to let Zemo rot in prison. Tony is almost able to overcome Bucky and Cap, and destroys Bucky’s bionic arm, but Cap manages to disable his armor, leaving him trapped and unable to finish the fight. He leaves his shield, and he and Bucky disappear. After returning home, while attempting to help Rhodes overcome paralysis after his injuries, Stark receives a letter of apology from Cap, and a phone in case he needs to renew contact, and Cap returns long enough to break the others out of prison before leaving with Bucky for Wakanda, where T’Challa agrees to keep him safe and in cryosleep until they can find a way to remove Hydra’s programming.
TLDR: After numerous large scale attacks the world comes together to ask super heroes to sign the Sokovia Accords, putting them under UN supervision, but Captain America refuses. Helmut Zemo initiates a plot to pit the Avengers against themselves, tearing the team apart.