Series 2 begins with Masters dealing with the ramifications of his disastrous presentation and being fired from the hospital. Meanwhile, Libby urges Masters to get another job; and Virginia fights off advances and innuendos stemming from the belief that she was the woman in Master's explicit film.
Betty's extortion continues as Masters starts his new job at Memorial Hospital and is told he can't continue to have Virginia as his secretary. Johnson doesn't know whether to get Masters to rehire her or to stay with DePaul as her condition worsens.
Virginia finds out about Masters' difficult childhood after they meet up at a hotel for a secret rendezvous.
Johnson and Masters are seen leaving a hotel together by Langham. Masters attempts bringing Johnson on board as his assistant as his new job. Betty tries to hide things from Gene.
Masters continues his work as the only white doctor in a black hospital, but it costs him his gynecology practice. Robert confronts Libby over the treatment of his sister. Betty and her former lover reunite. Johnson struggles to fix things with DePaul, who now knows what is going on with Masters.
Masters is banned from using black participants in his study, but he contacts a journalist to help him. Johnson is forced to accept DePaul's decision to stop her chemotherapy sessions. Gene finds out the truth about Betty and Helen's relationship.
Masters becomes impotent and stops his work with Johnson.
Johnson attempts to treat a woman on her own. Libby witnesses a hate-crime.
Masters isn't impressed at Frank's accusations. Virginia uses the case history of a patient in order to get some psychological advice. Betty and Masters think of a way to cure Lester's impotence and so hire him a prostitute. Barbara gets a unsettling diagnosis.
Johnson wants to find a cure for the difficulties that Masters is experiencing. Masters discovers a rival study. Langham is informed in order to keep his job, he has to have sex with Flo.
A television crew arrives to document Masters and Johnson's work.
Masters and Johnson feel ready to cure sexual dysfunction.