The full story
In 1946, Peggy Carter has been reduced to secretarial busywork at the Strategic Scientific Reserve, her wartime record with the SSR ignored by the men now running it. When industrialist Howard Stark is accused of selling weapons to America's enemies, he secretly asks Peggy for help clearing his name, revealing that his molecular nitramene formula has been stolen and weaponized. Working undercover with Howard's butler, Edwin Jarvis, Peggy traces the weapons to a Roxxon refinery and a Soviet operative named Leet Brannis, who works for a shadowy organization called Leviathan. Brannis is killed by his own handler, Sasha Demidov, before he can talk—but not before drawing a strange symbol in the dirt.
SSR chief Roger Dooley, agent Jack Thompson and agent Daniel Sousa open their own investigation, tracing the weapons to a ship marked with Brannis's symbol. Howard, resurfacing briefly, claims one of the recovered devices is a citywide blackout weapon—but Peggy discovers it's actually a vial of Steve Rogers's blood, and that Howard lied to keep her from finding it. Meanwhile, a new neighbor named Dottie Underwood kills a criminal stalking Peggy's apartment without a flicker of hesitation, revealing herself—though not yet to Peggy—as a trained Leviathan sleeper agent.
Decrypting a Leviathan cipher, Peggy learns Howard is set to sell weapons directly to the organization at a Soviet complex. There, she and the SSR discover a facility training young girls as sleeper operatives, lose a Howling Commando in the raid, and capture the facility's psychiatrist, Dr. Ivchenko. Sousa starts to suspect Peggy is the mystery woman who's been shadowing the case, and Underwood, searching Peggy's apartment, finds evidence tying her to the stolen weapons.
Ivchenko, secretly working for Leviathan, hypnotizes an SSR agent into revealing that only Dooley can access the vault holding Howard's remaining weapons—then makes him kill himself to cover the trail. Underwood knocks Peggy out and frames her; Thompson and Sousa arrest her. Peggy talks her way free by finally telling her colleagues the truth, and Jarvis buys time with a forged confession from Howard. It isn't enough: Ivchenko hypnotizes Dooley into stealing a weaponized nerve gas from SSR custody, and he and Underwood release it inside a packed movie theater, causing the crowd to turn on each other. Dooley, forced into an experimental Howard-built vest wired to detonate, jumps from a window to save everyone else in the room—killing himself in the blast.
The gas is identified as Midnight Oil, a wartime stimulant of Howard's that the military once used against Soviet forces at Finow, causing a massacre Ivchenko—revealed as Dr. Johann Fennhoff—has been avenging ever since. In the finale, Fennhoff kidnaps Howard and hypnotizes him into agreeing to drop a bomb of the gas on Times Square. Sousa stops Fennhoff; Peggy defeats Underwood, who escapes; and Peggy talks Howard back from releasing the gas. She throws Steve Rogers's blood into the East River, finally letting go of him. Fennhoff is imprisoned in the same facility as a captured Arnim Zola, who starts making plans of his own—the first seed of what becomes Hydra's Winter Soldier program—as Peggy's name, and Howard's, are quietly cleared.