Stabler is forced to adapt to massive changes both in his personal life and professional after returning home from a dangerous assignment. Bell hires an adviser whose AI technology program she hopes will revolutionize police investigation. Meanwhile, Jet and Reyes still struggle to deal with Whelan's absence nearly six months later.

When a local mosque is bombed, killing the imam, Stabler meets with Bashir, a hate crimes officer, who believes more is at play. Jet is keen on Vargas's program, but the others are more sceptical. Reyes struggles with his feelings with Jet. Stabler also reunites with Dr. Melinda Warner, who he hasn't seen in twelve years. Elliot's estranged brother Randall, is invited to NY by their mother, who wants to see him.

Stabler and Bashir search for a asylum seeker and his son who have gone missing from the mosque. This leads them to a smuggling ring using Afghani refugees to smuggle gems internally into the country. They break up the ring, kill those behind the bombing, and rescue the son who was being held hostage to coerce his father. Stabler learns that his younger brother Joe is back in NY.

The Widow Santos contacts Stabler and agrees to testify for Carisi against Los Santos and go into witness protection with her two children, because her family is being threatened by her brother-in-law. They stash the family in a safe house guarded by the team, except for Stabler who killed their father, until they can be picked up. Stabler has a family dinner at his house so the family can see his mother before she goes into a home. The dinner degenerates into drunken arguments and recriminations as secrets from the past are revealed. Stabler is called away when Los Santos storm the safe house after being tipped off by the daughter. During the firefight Stabler fights his way into the house and tries to get the Santos and the team out. The son picks up a gun and shoots Bell, and Stabler shoots him to stop him getting off another round. Bell is rushed to hospital and Stabler is suspended pending an IAB investigation into the shooting.

Bell is recovering in the hospital. Stabler is suspended and cleaning up after the dinner party when he finds some brown heroin. Jet and Reyes are questioned by IAB. A friend of Rita Lasku, the waitress Stabler helped while undercover with the Kostas, tells Stabler that Rita is missing and shows him a video of her at a party with the Westbook DA. Stabler turns up at the DA's house and asks about his friend Rita and is thrown in jail by Chief Bonner. Stabler discovers that a local waitress also went missing after a party, and her brother gives him her burner. Jet, Reyes, and Vargas have arrived after tracking Stabler's phone to Long Island. Stabler calls a number on the waitress's burner and is sent a video of Lasku tied up in a bunker. Stabler finds the bunker and frees the waitress who is tied up inside. He is attacked by the kidnapper, who escapes after a fight. Outside Stabler digs up Lasku's body in the sand. Chief Bonner takes over the investigation and more bodies are found in the dunes.