The film begins with Joe, portrayed by Joaquin Phoenix, in a rundown motel. Joe is a skilled hired gun, specializing in recovering missing trafficked girls. After successfully completing a job, he meticulously cleans up his traces before leaving. Canvassing the streets, Joe finds himself in a confrontation with an assailant in an alley, but he skillfully defends himself and escapes. He soon locates a phone to inform his handler that the mission is accomplished.
Living in New York City with his frail mother, Judith Roberts, Joe is not only a tough operator but also a son grappling with deep emotional scars. A former FBI agent and Gulf War veteran, he suffers from PTSD, haunted by eerie flashbacks — such as the disturbing memory of a child he saw shot after Joe offered him a candy bar, traumatic scenes from an abandoned storage unit with lifeless bodies of trafficked girls, and bleak childhood recollections of evading his abusive, alcoholic father. In moments of despair, he contemplates taking his own life, often playing with a knife or standing on the precipice of train tracks.
In another grim turn, Joe visits a local bodega to collect his payment from Angel, a middleman handling communications between Joe and his handler. During their exchange, Joe expresses concern that Angel’s son Moises saw him returning home the previous night, hinting that the boy might be aware of Joe's dangerous profession. Feeling uneasy about this, Joe decides to sever his ties with Angel.
Later, Joe meets with his handler John McCleary, who briefs him about a new assignment: he must locate the missing daughter of State Senator Albert Votto, whose daughter, Nina, has vanished. Votto wishes to avoid involving law enforcement, as he is collaborating with Governor Williams and offers a hefty sum of $50,000 for her safe return.
Upon meeting Votto, Joe learns the girl’s name and possible whereabouts, specifically noting a location notorious for sheltering trafficked girls. Votto urges Joe to punish those responsible once he retrieves his daughter. After scouring the area for supplies, Joe identifies the child trafficking hub that Nina is believed to be held captive in. The tension escalates as Joe confronts and intimidates a man for information on the number of guards present.
With steely determination, Joe infiltrates the house, eliminating any threats in his path until he finally locates Nina. He takes her to a motel, anticipating the arrival of her father, only to discover disturbing news on the television: Votto has apparently committed suicide. As chaos ensues, corrupt officers barge into the motel, seizing Nina from Joe. In a fierce struggle, Joe fights back and vanquishes one of the rogue cops.
Seeking assistance, Joe attempts to reach McCleary, only to learn that he has been killed, along with Angel and Moises. Returning home, Joe is met with the tragic sight of his mother, now lifeless in her bed. The perpetrators—still lurking—are confronted as Joe fights for survival, ultimately overpowering them. As one unfortunate assailant clings to life, Joe demands answers regarding his mother’s death and Votto's suicide. The hitman reveals a shocking truth: Votto was part of a larger conspiracy with Governor Williams, who had vested interests in Nina.
In a moment of profound grief, Joe buries his mother by a lake, momentarily overwhelmed by sorrow, he attempts to drown himself. However, a vision of Nina jolts him back to reality, reigniting his resolve to finish what he started. As the narrative unfolds, Joe pieces together the sinister plot—realizing that Votto had sold Nina to Williams to gain favor, a decision that drove him to despair and ultimately to self-destruction.
With newfound clarity, Joe tracks Williams throughout the city, only to discover his ultimate location—at home, met with shocking circumstances as he finds the decorated official dead, a victim of throat slitting. Amidst the eerie stillness, Joe uncovers Nina in the dining room, smeared in blood, holding a razor.
Joe then takes Nina to a diner to share a meal together. While she heads to the bathroom, an unexpected turn occurs when Joe shoots himself in his despair, unnoticed by the world around him. Yet, as Nina returns, reality shifts; the scene reveals that it was merely a fantasy, as Joe remains in a clouded state of exhaustion. She gently suggests a stroll, claiming it’s a beautiful day, and with that, they fade away from view as the camera lingers on their now-abandoned booth.
