In my opinion one of, if not the, best of the Marvel films to date, the Winter Soldier marked a critical change in the makeup of the MCU. This one is a bit long and detailed, but it’s worth it.
Captain America continues to work with S.H.I.E.L.D. and play catchup on the 21st century after the events of the Avengers and the previous Captain America movie. He briefly befriends former para-trooper Sam Wilson before being called into action to help rescue a captured SHIELD ship with the help of Black Widow and the STRIKE team, led by Rumlow. They are able to rescue the hostages and take out the pirates, but Widow is distracted in the middle of the mission, retrieving files for Fury, and it nearly costs them. On their return Cap is furious at Fury for not telling him about the side mission, leading Fury to share their upcoming initiative with him: Project Insight, three heavily armed new helicarriers with continuous flight capabilities, able to take out targets whenever SHIELD wants, anywhere in the world. Fury says that they are needed to keep the world safe, but Cap sees it as an end to freedom. Afterward Fury attempts to decode the data Widow recovered, only to find that he can’t. Concerned, he goes to Secretary Alex Pierce, his old friend and liaison to the security council, asking that Project Insight be put on hold.
Cap visits Wilson at the VA, wondering if he still has a reason to stay with SHIELD, but unable to make a decision. Fury hits the road and finds himself under attack and injured. He is able to hold the attackers off with moderate success and leads them on a harrowing car chase attempting to escape when he runs into the Winter Soldier. He is barely able to escape alive. Cap returns home and chats briefly with a neighbor before realizing that someone has broken in to his apartment. He sneaks in the side to find an injured Fury, warning him that SHIELD has been compromised. Fury is suddenly gunned down through the window, and manages to warn Cap to trust no one, and hands him the data drive from the ship before passing out. The neighbor, secretly a SHIELD agent assigned to guard and watch Cap rushes in to tend to Fury while Cap takes off in pursuit of the shooter. He finds the Winter Soldier, but is unable to capture him. They rush Fury to a hospital, joined by Widow and Agent Hill, but they are too late and Fury is pronounced dead.
Rumlow finds Cap and informs him that he is wanted for questioning at SHIELD, right away. Unsure of who to trust Cap stashes the data drive in a vending machine and goes to meet with Pierce. Pierce demands to know why Fury was in Cap’s apartment, but Cap won’t share. When he goes to leave Pierce orders him captured, leading to a fight between Cap and the STRIKE force in the elevator. Cap is able to break his way out of SHIELD headquarters, and is declared a traitor and enemy of SHIELD.
When Cap returns to fetch the data drive he finds that Black Widow already has it and wants to help him. The two track down the original location of the data, evading pursuit by STRIKE, and make their way to the military base where Steve was trained and find a secret underground SHIELD base. The computerized consciousness of Doctor Zola, the Hydra scientist, informs them that Hydra never really died, that they were reborn inside SHIELD, and have been working behind the scenes for the last seventy years, growing in power, manipulating world events. His villain monolog proves to be a diversion, keeping Cap and Widow at that location while he prepared to blow the place and kill them. Fortunately Cap is able to save them and they slip away.
They lay low at Wilson’s place and recruit him for help in finding out what’s going on. They steal his old gear, a set of experimental mechanical Falcon wings, and go after the one SHIELD agent they know for sure is actually Hydra: Jasper Sitwell. They kidnap and interrogate Sitwell, learning that the plan is to use Project Insight to eliminate all of Hydra’s enemies and potential enemies, using an algorithm created by Zola. They plan to use Sitwell to get them into SHIELD headquarters, but the Winter Soldier shows up and kills Sitwell before turning his sights onto them. They manage to fight him off for a while, but during the fight the Soldier’s mask comes off and Steve recognizes him as his old friend Bucky Barnes, believed to have died back in the war, but apparently a victim of Hydra science. With the distraction of Bucky’s resurrection, Cap, Widow, and Falcon are captured. Fortunately for them, the transport is infiltrated by Agent Hill and they secretly escape before reaching their destination.
Hill takes them to a SHIELD black site and reveals that Fury isn’t actually dead, the doctors faked it so the enemy would believe the assassination was successful. The group puts together a plan to reprogram Project Insight and sets out to infiltrate and destroy SHIELD. As Pierce hosts the security council, Cap and Falcon break into the facility and alert SHIELD to Hydra’s presence, turning the agents on each other and attempting to prevent the launch of Insight. Hydra is able to launch anyway, leading Cap and Falcon on a mad race to get on the helicarriers and swap out their targeting programs. Cap takes care of one of the carriers, and after a lot of gunfire Falcon is able to reprogram the second. When Falcon flies Cap to the third one they run into the Winter Soldier, who pulls off Falcon’s wing, sending him parachuting down and grounding him. Cap manages to barely hang on after getting thrown overboard and makes his way to the computer, only to see Bucky again.
Meanwhile in light of Cap’s message about Hydra being in SHIELD, the Security Council is held hostage by Pierce. He threatens to kill one of them and Widow reveals that she has infiltrated the council. She holds Pierce at gunpoint and begins to upload SHIELD and Hydra’s secrets to the internet, exposing Hydra to the world along with her own sordid past. Fury arrives to give the final security clearance and the secrets are out. Rumlow is called by the other Hydra officers to secure Pierce and the council, but is intercepted by Falcon. Pierce tries to escape, using Widow as a shield, but she electrocutes herself to disable the bomb he planted on her, and Fury takes him out.
Cap manages to switch out the final targeting chip just as the Insight system is finding its first batch of targets, switching the thousands of original targets to just three: the insight helicarriers. The carriers take themselves out of the air, sending them crashing into the water around the SHIELD base, and into the SHIELD base itself. Rumlow and Falcon make a desperate run of it to get out of the way of the crashing ship. Falcon manages to leap to Fury and Widow’s helicopter at the last moment, but Rumlow is caught in the rubble. Cap remains on the other ship, attempting to free a pinned Bucky and bring him to his senses. Bucky plans to complete his mission and kill Cap, but can’t quite bring himself to do so, instead watching as Cap gets knocked into the water below, and jumping in after to rescue him before disappearing.
With the information out in the world, many Hydra members are arrested, and Widow testifies before congress. Former SHIELD agents move on to other agencies and other jobs, but Fury knows there are more Hydra agents out there. Cap and Wilson turn down his request for help, instead planning on tracking down Bucky.
Bucky, on the other hand, now free of Hydra’s control, sets out to try to discover who he was, and who he is.
TLDR: Hydra lives on, hidden within SHIELD. They plan to control the world with giant gunships, but Fury and then Captain America are on to them. Cap joins up with Black Widow, unsure who else to trust, and gains a friend in Falcon, and they are able to take down Hydra and SHIELD.