The movie opens with Yelena Belova (Florence Pugh) infiltrating a secret laboratory. She skilfully neutralizes several guards, displaying her combat expertise, before locating the research and artifacts she was assigned to retrieve on orders from Contessa Valentina De Fontaine (Julia Louis-Dreyfus), working for the OXE Group. During her mission, a scientist attempts to stop her, warning about Valentina’s work on a dangerous project called “Project Sentry”, but a fight ensues, culminating in the scientist accidentally shooting himself. Yelena escapes with the necessary items and destroys the lab, then reports back to Valentina about her success.
Meanwhile, in Washington D.C., Bucky Barnes (Sebastian Stan) now serves as an elected congressman. He is involved in a trial where Valentina faces impeachment due to her secretive operations. She is accompanied by her loyal assistant, Mel (Geraldine Viswanathan). Valentina justifies her actions by referencing past incidents, such as the Red Hulk event, emphasizing that the Avengers are no longer around to handle global threats, hence her justification for her controversial actions.
Yelena visits Alexei Shostakov (the Red Guardian, played by David Harbour) at his home, where he lives alone. She confesses her disillusionment with her years of service and reveals the emotional burden she carries following Natasha's death. After their conversation, Yelena contacts Valentina to receive her next assignment, which involves targeting a character named Ava Starr — Ghost (Hannah John-Kamen).
Upon reaching her target, Yelena finds herself attacked by John Walker — U.S. Agent (Wyatt Russell), who fires at her. The chaos intensifies when Antonia Dreykov — Taskmaster (Olga Kurylenko) joins the fight, with each combatant exchanging gunfire. During the skirmish, Ava reappears and shoots Taskmaster in the head. The confrontation reveals a mysterious civilian survivor, Robert “Bob” Reynolds (Lewis Pullman), and the others quickly deduce that Valentina sent them to eliminate each other. They discover that the artifacts in the lab are property of the OXE Group, and Valentina is trying to erase evidence, including the deceased assassins.
In a flashback, Yelena experiences vivid memories of her childhood, specifically her origin in the Red Room, where she was manipulated into executing her first victim, a girl named Anya, at a young age. She snaps out of her emotional recollection after touching Bob’s hand, which triggers the memory. Together, Yelena, Walker, Ava, and Bob attempt to escape The Vault by climbing up the walls, a feat achieved by locking arms and walking vertically. During their ascent, Walker glimpses a shameful memory of himself arguing with his wife about neglecting their son for his duties, revealing the personal toll of his role as a hero.
While this chaos unfolds, Valentina hosts a glamorous gala where she and her assistant Mel are present. Bucky Barnes also attends, collaborating with Congressman Gary (Wendell Pierce) to bring Valentina down. Bucky approaches Mel and shares his contact information, hinting at potential collaboration outside her allegiance. Mel later reports to Valentina via surveillance footage that the targets — Yelena, Walker, and Ava — have united, prompting Valentina to send mercenaries after them. She also instructs her team to keep Bob alive due to his status as a survivor of the experiments.
As Valentina’s mercenaries close in, the team makes a daring escape. They disguise themselves in armor, but the guards catch them. To protect her allies, Bob exits their vehicle and draws enemy fire, remaining unharmed despite being shot at, which surprises Valentina. Witnessing his resilience, Bob flies high into the sky but faints from exhaustion and crashes back into The Vault, where Valentina’s team captures him.
The group—Yelena, Walker, Ava, and Alexei—flee across the desert, contemplating their next move. Ava remarks on Taskmaster’s tragic circumstances, pointing out that her own situation mirrors their struggles. The next morning, Alexei, disguised as Valentina’s limo driver, finds and rescues Yelena. Though he is awkward with the vehicle, they manage to escape as a convoy of mercenaries pursues them, firing from their vans. Ava attempts to use her powers but is blocked by a sonic ray. Their salvation comes when Bucky, wielding grenades, destroys the pursuing vans, although he inadvertently causes the limo to flip over.
Meanwhile, Bob wakes up to find Valentina herself waiting for him. She manipulates him by convincing him that, as Sentry, he has nearly godlike powers. She touches his hand and recalls her own traumatic childhood, revealing her troubled past. Bob agrees to her persuasion, promising to keep his powers under control.
Bucky captures and interrogates Yelena, Alexei, Walker, and Ava, and upon learning about Valentina’s plans for Bob, he rushes to stop her. Valentina defends her actions, claiming that her goal is to prevent worse threats by creating her own team of heroes she calls “The New Avengers”—a nod to her scheme and the official title of the film. She argues that her plans are for the greater good, even as her motives remain ambiguous.
In an intense confrontation inside Valentina’s base, dubbed the Watchtower (the former Avengers headquarters), the team faces off against Valentina and her mercenaries. They clash with her elite guards, leading to a fierce battle. Valentina unleashes Bob, now transformed into Sentry, who proves overwhelmingly powerful, even ripping off Bucky’s vibranium arm. The team’s attacks are futile, and Sentry begins to turn against her, believing he no longer needs her commands. Just as Bob aims to choke Valentina, Mel intervenes with a killswitch, knocking him out and ending his rampage. As Valentina and Mel depart, Bob’s body is enveloped in darkness, signaling a darker emerging threat.
Outside, the team is disheartened, feeling their efforts have been futile since they are only beginning to understand their own limitations. Alexei approaches Yelena, who is overwhelmed with feelings of loneliness and regret about her life apart from her work. He gives her an uplifting speech, reminding her of her value beyond her job. Just as Yelena starts to feel hopeful, they look up in awe to see Sentry, now transformed into The Void, spreading shadows over New York City using his immense powers.
The remaining Thunderbolts, as the team is colloquially nicknamed, rally to protect the populace, but The Void plunges the city into darkness. Yelena decides to confront The Void directly, entering his mindscape. She fights through traumatic memories, including her childhood in the Red Room and her relationship with Natasha. In a pivotal scene, she encounters Bob’s sorrowful memory, where he is abused by his father and blamed by his mother. She urges him to face his feelings instead of suppressing them, leading to a heartfelt group effort to pull him out of The Void. Their collective support calms Bob, restoring peace to the city and freeing the citizens from darkness.
After their victory, Bob wakes up with no memory of what happened. The team then turns their attention to Valentina, who cleverly covers her tracks by holding a press conference, announcing her team as the next wave of Avengers—a title that hints at her true plans and signals the formation of “The New Avengers”, the film’s subtitle. During the event, Yelena reminds Valentina that her control over the team makes her responsible for them now.
The mid-credits scene shows Alexei at a supermarket, where he spots the New Avengers featured on a Wheaties cereal box, humorously referencing a previous line. He tries unsuccessfully to get recognition from a woman there.
In the post-credits scene, set 14 months later, the public’s reception of the New Avengers is mixed—some see them as heroes, others remain skeptical. Bob, now struggling to keep his powers in check to prevent The Void from returning, faces ongoing challenges. The team detects a space crisis, with an unidentified spacecraft entering Earth’s atmosphere, bearing a strange symbol—a large “4” on its side. The scene builds anticipation for future adventures, hinting that the New Avengers and Bob will return to face new threats yet to come.