On June 12, 2014, the disappearance of three Jewish boys in Israel sends shockwaves across the nation. Simon, a terrorism agent at the Jewish Division of Shin Bet (Israel Security Agency) and his team search for answers. Arab teen Mohammed lands in a dangerous environment while Jewish teen Avishai finds himself at a crossroads.

In the wake of their son's disappearance, Hussein and Suha face pressure from the police as they search for answers. Simon and Mike disagree on their theories about the murder and a new angle arises when a rumor leaks to the public.

Simon meets with Mohammed's family to probe for details about his life. Hussein and Suha find their neighborhood in the midst of a riot, while misinformation spreads across the internet.

With the Jerusalem deputy DA looking over their shoulders, Simon and his team focus their investigation on Israeli persons of interest as Mohammed's family remain overwhelmed by the fervor surrounding their son's death.

Mike worries that Simon risks crossing a line when he goes undercover as a reserve-duty soldier in Adam to learn more about Yosef and Rabbi Yizhak Ben Shoshan. Later, Simon works to get a tortured Avishai to open up to him, as Shabak readies to make crucial arrests. Suha mourns Mohammad's death and learns more about his life, and Hussein decides to talk to the media.

While investigators struggle to get confessions before lawyers come into the picture, Simon reveals his true identity to Avishai and asks for Dvora's help in getting the teen to break his vow of silence. Hussein is approached by prosecutor Uri Korb, as riots spread throughout the West Bank and Muhammad becomes a symbol of the Palestinian national struggle.

Avishai takes Simon through the sequence of events that led to Muhammad's kidnapping and murder, revisiting key locations and recreating the crimes for police cameras. Desperate for atonement, a guilty Avishai slowly pieces together what happened, as Simon begins to realize the extent of his involvement in that fateful night.

Avishai and Yinon spend their first days in prison in isolation out of fear of retaliation by other prisoners, and Avishai tries to get in touch with Simon, who finds that his role in the case has turned personal after he receives a visit from his brother, Rami. Dvora stands her ground against Asher Ohayun, a religious defense lawyer working to get him declared insane.

As the trial begins and Yosef puts on an act of insanity, Avishai's lawyer instructs him to set himself apart from Yinon, but when Avishai asks Yinon to support his version of events, the two get into a harsh confrontation. Simon takes the stand and is pressed about Avishai's culpability in the murder. Dvora sees the consequences of not cooperating with the rabbis in the orthodox community.

As the trial reaches its climax, a psychologist speaks to Yosef's mental state, while an emotional Avishai prepares for his testimony and a tough cross-examination; Simon finds that his good work has come at a price.