In the sweltering streets of Harlem in 1989, we encounter John Shaft, portrayed by Samuel L. Jackson, who finds himself deep in a heated argument with his partner Maya Babanikos, played by Regina Hall. Just as tensions rise, they are thrust into a dangerous situation when a group of heavily armed assailants confronts them. With lightning-fast reflexes and a keen sense of danger, Shaft is able to protect Maya, eliminating the threat that looms over them. During their frantic search for answers, they stumble upon a shocking stash of illegal drugs tied to the notorious crime lord Pierro "Gordito" Carrera, depicted by Isaach De Bankole. As Shaft attends to Maya, it soon becomes apparent that their young son, John Jr. (or JJ), played by Jessie T. Usher, was blissfully unaware of the chaos that unfolded, comfortably seated in the backseat. This close encounter leads the couple to a pivotal realization: their life entangled in danger cannot coexist with raising a family, leading to their reluctant separation, leaving Shaft to reflect on the repercussions of his choices.
Fast forward twenty-five years, and Shaft's life is a well-kept secret from JJ. Nevertheless, he continues to show affection through gifts like a Super Bowl ring and a box of condoms, reminders of their bond. Now a graduate from MIT, JJ has made a name for himself as a cybersecurity expert with the FBI, surrounded by friends Sasha Arias (Alexandra Shipp) and Karim Hassan (Avan Jogia). Under the watchful eye of Special Agent Vietti (Titus Welliver), JJ discovers the necessity of monitoring the Rashad Azzam Mosque and its Imam Farik Bahar (Amato D'Apolito), noted for his suspicious trips to Afghanistan. Despite intentions to avoid any appearance of Islamophobia, JJ's desire to investigate intensifies, only to be met with resistance from Vietti, who deems him unqualified.
One night, JJ meets with Sasha and Karim in a local bar, where Karim discusses his recovery program called Brothers Watching Brothers, aimed at helping veterans with addiction issues. After Karim departs unexpectedly, JJ's concern for his friend's well-being compels him to track him down, but the next day he receives devastating news from Maya: Karim has been found dead. The somber tones of a funeral echo as friends, family, and fellow marines pay their respects to Karim. JJ, lost in thought, studies the crime scene report, connecting Karim's overdose to Manny Orozco (Ian Casselberry), a powerful figure in the underworld.
Driven by a need for justice, JJ embarks on a quest for answers, utilizing help from a neighborhood kid to locate Manny. However, he is ambushed by one of Manny's henchmen, leaving him injured and hospitalized. While recovering, JJ confides in Sasha about his struggles to gain information from Manny. This leads him to seek help from the only person who might be able to help him—his estranged father, Shaft, referenced by Richard Roundtree.
Their first meeting is filled with tension, yet JJ begs for his father's aid in solving Karim's murder. Noting JJ's injuries, Shaft takes it upon himself to guide his son, leading him back to the crime scene. There, Shaft's skills allow him to confront Manny's men effectively, while the notorious Manny is already aware of Shaft's reputation and attempts to vanish. Nonetheless, Shaft captures Manny and extracts critical information about Karim's last moments. As father and son navigate their complexities in pursuing justice, JJ advocates for a gentler approach, whereas Shaft embraces his trademark aggression.
Their journey takes them to the rehabilitation center where they meet Karim's comrades Major Gary Cutworth (Matt Lauria), Sgt. Keith Williams (Robbie Jones), and Staff Sgt. Eddie Dominguez (Aaron Dominguez). The heart-wrenching stories shared about Karim's fervor post-conversion reveal much about his character and his introduction to Anam (Almeera Jiwa) at the mosque. As their discussions wind down, Shaft decides it's time for JJ to experience the nightlife of the city. When they visit a glamorous nightclub, JJ's encounter with partygoers Baby (Chivonne Michelle) and Sugar (Tashiana Washington) spirals into chaos when JJ, fueled by confidence, finds himself in the middle of a fight, only to end the night by embarrassing himself and his father.
The following day, they aim to gain access to the mosque, but face resistance from Farik, Anam's father, who is quick to dismiss them upon discovering JJ's FBI ties. Undeterred, JJ dives into the mosque's financials and uncovers suspicious transactions from a new supermarket. Reporting his findings to Vietti leads to a shocking consequence—JJ is put on administrative leave for overstepping his boundaries.
In a twist of fate, Shaft and JJ confront the supermarket manager, Bennie (Luna Lauren Velez), who initially presents as pious but soon reveals her questionable dealings, sparking suspicion that the establishment may be a front for Gordito's drug operations. As they gather intel, JJ cleverly installs a micro-camera to unveil Bennie's secrets.
Later, during an ill-fated dinner date with Maya, the reprieve is shattered when armed gunmen invade the restaurant, prompting Shaft to spring into action to protect Maya. Simultaneously, JJ's night out with Sasha turns disastrous as he finds himself embroiled in a related skirmish. After reuniting, JJ's investigation leads them to a chilling revelation—Bennie orchestrated the attack on their family.
A major raid at the mosque culminates in Farik's arrest. This ignites a firestorm of backlash for alleged Islamophobia, resulting in JJ's termination from the FBI, deepening the rift between him and his father. As the story unfolds, JJ grapples with betrayal and isolation, while Shaft's attempts at connection seem futile, often backfiring.
Desperate to seek guidance, JJ, Shaft, and Shaft Sr. (Richard Roundtree) join forces, armed with insight from their elder. They embark on a dangerous mission to confront Gordito and his enforcer cutty. Breaking into Gordito's stronghold, they fight a fierce battle against overwhelming odds. With quick thinking and skill, JJ confronts his adversaries, ultimately saving Sasha and avenging Karim's death, although at a costly price. Shaft is gravely injured protecting JJ, leading to a tense standoff that sees the demise of their enemies.
As the dust settles, Shaft awakens to the relieved faces of JJ, Shaft Sr., and Maya, who expresses a newfound softness towards him, recognizing his sacrifice. In a moment of happiness, JJ seals his relationship with Sasha, greeted with smiles from his father and grandfather.
Returning to the FBI amidst applause, JJ's choice to abandon formal law enforcement for the life of a vigilante alongside his father and grandfather marks a poignant turning point. Together, they step boldly into the tumultuous streets, united in their quest for justice.
