In 1989, private investigator John Shaft II, alongside his wife Maya Babanikos and their infant son, JJ (John "JJ" Shaft Jr.), narrowly escapes an assassination attempt by the ruthless drug lord Pierro "Gordito" Carrera. Fearing for their safety due to Shaft II's dangerous lifestyle, Maya makes the difficult decision to leave him, choosing to raise JJ on her own.
Fast forward 25 years, and JJ, portrayed by Jessie Usher, has become a skilled FBI agent and cybersecurity expert, armed with a degree from MIT. The sudden death of his childhood friend Karim Hassan, ruled as a heroin overdose, sends JJ spiraling into suspicion—he believes that Karim was murdered rather than succumbing to addiction. With determination, JJ returns to Harlem to confront Manuel, a local drug dealer linked to Karim's death, but ends up being violently thrown out of Manuel's territory.
In the hospital, while recovering from a minor injury thanks to his childhood crush Sasha Arias, JJ learns from her that the heroin levels found in Karim's toxicology report indicate possible foul play. Driven by concern, JJ seeks the help of his estranged father, Shaft II, who agrees to aid in the investigation after uncovering potential leads pointing to Gordito.
As the duo—Shaft II with his old-school grit and JJ with his modern sensibilities—delve deeper into the case, they explore "Brothers Watching Brothers," a rehabilitation clinic connected to Karim. Here, they discover that Karim had become disenchanted with rehab and turned to a mosque, which has drawn the FBI's attention over alleged ties to terrorism.
Their investigation takes a romantic turn when Shaft II nudges JJ and Sasha into going on a dinner date, adding tension and flirtation to the proceedings. They also chase leads involving Bennie Rodriguez, the mosque’s benefactor, played by Lauren Vélez, after learning about her significant donation of $500,000. Meanwhile, Maya calls to announce her arrival in New York for a date, uncertain of the dangers surrounding her family.
Escalating threats see Shaft II and JJ dodging multiple assassination attempts, instigated by Bennie. To protect JJ, Shaft II makes the tough choice to exclude him from the investigation temporarily. After confronting the FBI's handling of their findings—which leads to a public outcry against supposed Islamophobia causing JJ’s dismissal—JJ believes Shaft II might be manipulating him, leading to conflict in their relationship.
When Shaft II reconciles with Maya, JJ and Sasha race against time to uncover the truth behind the mosque and Karim's death. They learn that the clinic serves as a façade for a drug trafficking operation involving military-grade vehicles used to smuggle drugs into the U.S. This operation, orchestrated by Bennie, leads to Karim’s tragic demise when he threatened to expose them.
As tensions mount, JJ finds himself captured by smugglers, while Sasha faces peril of her own. In a dramatic turn, Shaft II comes to their rescue with the firepower of John Shaft Sr., JJ’s grandfather, as they launch an assault on Gordito’s penthouse. In a gripping showdown, Shaft II courageously takes a bullet meant for JJ, ultimately defeating Gordito and ensuring justice is served.
In the aftermath, as Shaft II recovers at the hospital, a newfound romance blossoms between JJ and Sasha. While JJ is offered his job back at the FBI, he chooses to reject it, opting instead to join his father and grandfather in their private investigation business, embracing his family legacy.
