Flashbacks introduce a young Kurt Weller at military school in 1996, when he first meets Shepherd. In the present day Weller, Jane and Nas return to the school looking for answers. The commandant says Shepherd's real name is Ellen Briggs and that Ellen funded his entire education. Nas then confirms Ellen was a Major General and head of a key government agency.
The team finds one lead in her history: a retired military officer named Sean Clark. Clark is brain-damaged after a stroke but Patterson uncovers a conversation between him and Bethany Mayfair, where Clark insisted Weller stay in New York instead of promoted to a higher position in Washington D.C., thus ensuring he'd be there to find Jane.
Clark tells Weller about "the Truman protocol." But before he can get details, Weller finds Shepherd waiting in Clark's room at the assisted living facility. She kidnaps both of them, kills Clark and tells Weller they'll meet again.
Reade, Zapata and Patterson investigate the tattoo clue of the week. It involves a Bible verse that does not exist and a farmer named Jarrod. Jarrod's farm it's full of weapons and bomb-making materials. Jarrod himself then shows up in their office saying he's an FBI informant charged with staging a domestic terrorist attack under another secret program.
Jarrod is killed when one of his co-conspirators blows his cover and escapes. Weller fires the agent in charge of the program and sends his team after Tess, who is targeting a federal building with a truck full of explosives. But he talks her down by appealing to her military past.
And Roman, having seen Shepherd's files thanks to Nas, questions why he would have followed his foster mother in the first place. Plus Reade's affair with Freddy's ex-girlfriend takes a turn when she convinces him to try cocaine, and Jane goes on another date