In 1989, John Shaft II (Samuel L. Jackson) (a private investigator), his wife Maya Babanikos (Regina Hall), and his infant son John "JJ" Shaft Jr. survive an assassination attempt by drug lord Pierro "Gordito" Carrera (Isaach De Bankolé). Concerned that Shaft II's lifestyle will put them in danger, Maya leaves him and raises JJ on her own. 25 years later, JJ (Jessie Usher) is an FBI agent and a Cybersecurity expert with a degree from MIT. After his childhood friend Karim (Avan Jogia) dies of a heroin overdose, JJ concludes he must have been murdered. JJ travels to Harlem to investigate Manuel, the drug dealer who runs the neighborhood and sold the heroin that allegedly killed Karim but is violently ejected from his property.While being treated for a minor injury in the hospital by JJ's other childhood friend and his own crush Sasha (Alexandra Shipp), he shows her Karim's toxicology report. She notes that the amount of heroin in Karim's system would have killed him long before he could have taken that much by himself, suggesting that he was indeed murdered. With no other recourse, JJ turns to Shaft II for aid. Shaft II agrees to help after realizing that JJ's case may lead him to Gordito. The two begin investigating together, but JJ's progressive white-collar outlook on life clashes with Shaft II's old-school street ways. After confronting Manuel again, the Shafts investigate "Brothers Watching Brothers", the drug rehab clinic Karim was a part of. There they learn that Karim stopped going to rehab in favor of attending services at a mosque currently under suspicion by the FBI for terrorism.The next day, Sasha accompanies JJ and Shaft II to investigate the mosque, where they are ejected from the premises after the imam notices JJ's FBI badge. Shaft II convinces JJ and Sasha to have a romantic dinner together, and the Shafts next investigate a convenience store owned by a woman named Bennie Rodriguez (Lauren Vélez) who donated $500,000 to the mosque. Maya calls JJ to inform him that she is coming to New York to meet a man for a date; she is overheard and followed by Shaft II. The Shafts survive two separate assassination attempts orchestrated by Bennie, and Maya forces Shaft II to kick JJ out of the investigation for his own safety.JJ turns over the evidence they have gathered to the FBI, who arrest the mosque's imam. However, the media accuses the FBI of Islamophobia, and JJ's boss Vietti (Titus Welliver) fires him. JJ returns to Shaft II and overhears a conversation about Gordito, leading him to believe that his father was stringing him along the entire time. Shaft had also figured that Bennie was Gordito's cousin.While Shaft II visits and reconciles with Maya, JJ and Sasha track down Bennie to an abandoned warehouse and learn that "Brothers Watching Brothers" is a front for a drug smuggling ring backed by Bennie; Karim was killed when he threatened to blow the whistle on their operation of purchasing broken army vehicles in Afghanistan, filling them with drugs and bringing them to US under guise of helping train veterans for vocational jobs. The $ 500 K was Karim's share which he refused to accept. So, Bennie transferred the same to the mosque that Karim supported. But he was killed by his comrades at "Brothers watching Brothers", who didn't want any loose ends.JJ is caught by the smugglers; Sasha is captured while JJ is rescued by Shaft II. The two visit JJ's grandfather, John Shaft Sr. (Richard Roundtree), to acquire more firepower, and Shaft Sr. decides to accompany them in an assault on Gordito's penthouse. The Shafts kill the drug smugglers and rescue Sasha before being confronted at gunpoint by Gordito. Gordito attempts to shoot JJ to spite Shaft II, but Shaft II takes the bullet and knocks Gordito out of a window to his death before collapsing. In the aftermath, Shaft II recovers at the hospital. JJ and Sasha kiss and begin a relationship. Vietti offers JJ his job back, but JJ turns it down in favor of joining his father and grandfather in their PI business.