Sherlock fills in Joan about the substance of his father's visit: that Morland is willing to restore them to their consultancy gig at the NYPD. Sherlock is hesitant because Morland's favors always come with a cost.
Meanwhile, the pair join up with Special Agent Gary Burke of the FBI to investigate the murders of two DARPA scientists and a student, plus the theft of hard drives containing sensitive research data in the area of brainwashing.
The first suspect is Dan Zheng, a Chinese diplomat who was romancing Dr. Sarkisian, one of the researchers. They locate the hard drives, but Sherlock figures out that the great brainwashing algorithm was a total flop, and Zheng knew it, and therefore had no motive.
A conversation with Sarkisian's ex-husband points them at Meher, Sarkisian's boss at DARPA, but he had nothing to gain and everything to lose by the resulting mess. Finally, they realize that one person did gain by what had happened: Alta Von See, another promininent DARPA official, who was now in the golden spot to be appointed head of DARPA.
She used an experimental device to incapacitate the researchers, allowing her to kill them. Unfortunately for her, she unintentionally did in the lab rat, too.
Sherlock decides to accept his father's offer to rejoin the NYPD, though Joan warns Morland not to hurt his son.