Retired schoolteacher Eloise Parker lives by herself in the Massachusetts countryside, but she has a tenant in her barn, Adam Clay, leading a quiet life as a beekeeper. One day, Eloise falls for a phishing scam and is robbed of over $2 million, the majority of which belongs to a charity organization she manages. Devastated, she commits suicide. Clay finds her body and is immediately arrested by FBI agent Verona Parker, Eloise's daughter. After Eloise's death is ruled a suicide, Clay is released. Verona tells him the group that robbed Eloise has been on the FBI's radar for a while but is difficult to track. She is pessimistic that they will ever be brought to justice even if they are found. Wanting justice for Eloise, Clay contacts the Beekeepers, a mysterious group, to find the scammers responsible.

Clay receives an address for the scammers: a call center run by Mickey Garnett. Clay scares off the employees and destroys the building. Garnett informs his boss, technology executive Derek Danforth, who sends Garnett to kill Clay. A violent confrontation ensues where Clay kills Garnett's men and severs Garnett's fingers. Garnett calls Danforth while stopped at a bridge, informing him that Clay is a Beekeeper. Having followed Garnett, Clay drags him off a bridge with a truck to his death and warns Danforth that he is coming after him.

Danforth informs former CIA director Wallace Westwyld, who is currently running security for Danforth Enterprises at the request of Derek's mother Jessica, about Clay. Concerned, Wallace contacts the current CIA director in hopes of stopping Clay. The director contacts the Beekeepers and learns that Clay has retired from the organization. The Beekeepers subsequently declare neutrality after Clay kills a Beekeeper sent to kill him. Meanwhile, Verona and her partner, Matt Wiley, anticipate that Clay will deliver an assault on the Nine Points Center in Boston, which oversees all of Derek's global scam call centers. After informing FBI Deputy Director Prigg that Clay is a Beekeeper, they receive full funding.

Wallace coordinates a group of ex-special forces personnel, revealing to them that the Beekeepers are a highly skilled and dangerous clandestine organization tasked with protecting the United States, operating above and beyond governmental jurisdiction. To have a chance at stopping Clay, Wallace orders the group to secure the inside of the Nine Points Building, while the FBI places their own SWAT team around the perimeter. Danforth's decision to not evacuate the employees enables Clay to quickly defeat the FBI SWAT team and infiltrate the building, taking down the manager, who reveals to Clay and the FBI that Danforth is his boss.