In bed together, Rigsby and Van Pelt are awakened in the early morning by Lisbon. They are to report to a crime scene. As Jane arrives at the same crime scene, he receives a call from Bosco who wants to talk to Jane but wants to discuss it in person at CBI Headquarters. Bosco, his team, minus Agent Hicks, and Rebecca the secretary are already at work.
Jane, Rigsby, Van Pelt and Cho are gathered at the crime scene. It is a cemetery where they find a body that is a nude male, sitting on the floor, and his genital area is covered with an arrangement of yellow roses. On discovering that the man had been frozen and placed in position, Jane comments that the body was intentionally staged to make some sort of statement. They depart the crime scene to return to CBI Headquarters.
At CBI Headquarters, Lisbon joins Cho and Jane where they encounter Bosco's secretary, Rebecca carrying coffee to Bosco's office. On entering Bosco's office, Rebecca screams and drops the coffee at the sight of her boss and two other agents that have apparently been shot. Two of the agents are dead and Bosco is barely alive. Lisbon begins Basic Life Support on Bosco while Cho takes charge of the situation to lock down the building. Jane appears stunned by the scene.
The storyline flashes back to the previous 24 hour period where Lisbon catches Bosco and Hicks raiding the staff refrigerator. Lisbon and Rebecca tease Bosco about telling his wife that he is cheating on his diet.
The storyline returns to the shooting scene where Bosco is being stabilized for transport by the paramedics. Jane still appears stunned but he has noticed that Agent Hicks is not among the victims. Lisbon prepares to notify Cho as to Hicks' whereabouts when Jane tells her she needs to clean up from all the blood on her clothes and face.
In the restroom, Lisbon is washing her blouse in the sink when she notices the blood on her face. As she stares in the mirror, she momentarily appears as if she is going to break down but then apparently stiffens her resolve as she continues to wash the blood from her blouse.
Lisbon and Cho question Rebecca. The only thing she discloses is that Bosco was working a development in a case involving an Armenian drug cartel. Jane appears and inquires as to the identity of the frozen body found earlier in the day. Lisbon appears agitated and tells Jane that the body identification is not a priority.
Meanwhile, Van Pelt and a security officer are reviewing camera footage of the building to uncover any unusual activity during the crime's time frame. Rigsby joins them to help. Van Pelt realizes that the computer's firewall has been breached when she tries to look at footage from the garage's cameras. There is a large time gap on those particular cameras and no way to tell what may have occurred in the garage.
Lisbon continues to follow-up the information on the drug cartel when she is approached by Minelli. He tells her that Bosco's injuries are extensive and she needs to prepare herself for the worst. He also wants to know if she can put personal feelings aside and handle the role as lead agent on the case. She assures Minelli that she can.
Lisbon, Cho, and Rigsby are discussing updated information about the Armenian drug cartel to determine if there may be a link to the attack at CBI Headquarters. Jane interrupts and again asks about the identity of the frozen body. Lisbon gets perturbed at Jane's persistence about the body's identification. Jane tells her that he is possibly related to the attack. Cho checks the forensics data base and learns that the victim's name is Dr. Towlen Morning. Jane appears to recognize the name and quickly leaves the office. Lisbon and Cho also leave to follow Jane.
Jane goes directly to the location of the doctor's office. Lisbon and Cho are not far behind. As Jane proceeds to the office, he notices a vase of yellow flowers sitting on a chair outside the entrance to the building where the doctor's office is located. He continues to rush to the office only to find the outer door locked. He quickly picks the lock and walks toward the examination room. As he is about to enter the room, he suddenly stops and appears shocked about something. Jane can see through the glass window of the exam room. It is a smiley face painted in what appears to be blood. As Jane opens the door he can hear music playing in the background. It is "Well-Tempered Clavier," Prelude 1 in C Major, by Johann Sebastian Bach. This is the same piece that Rosalind Harker (Alicia Witt) played for Jane in the Season 1 finale. Harker was romantically involved with Red John and had told Jane that Bach was Red John's favorite composer. Jane continues into the room and finds Agent Hick's body stretched out on an examination table. Lisbon and Cho finally arrive and see what Jane has discovered.
Outside the office building, Jane, Lisbon, and Cho discuss this development in the Red John case. Jane is puzzled but then realizes that Towlen Morning was the family physician for Red John's third and fourth victims nine years previously. The victims names were Carter and Janet Peak. Carter Peak's body was never found. Jane hypothe that Carter Peak's body was removed to cover a mistake that Red John had made, such as leaving behind DNA. Lisbon tells Cho to go through all of the doctor's records on Carter and Janet Peak.
Meanwhile, at CBI Headquarters, Minelli is giving a press conference about the day's events. When asked by one reporter how he feels, Minelli emotionally chastises the media for asking such idiotic questions over the years. After the press conference, Lisbon gives Minelli some uplifting encouragement.
Jane goes to the hospital to check on Bosco. The doctor informs Jane that the prognosis is not good. Jane tells the doctor that Bosco was in much pain and asks about his morphine dosing. Jane used the question as a ruse so the doctor would identify which device was the morphine pump. The doctor leaves the room and Jane proceeds to unplug the pump.
Lisbon enters the hospital room and confronts Jane's plan to wake Bosco for information about the shooting. Lisbon accuses Jane of being cold-hearted and Jane tries to convince Lisbon that Bosco would want to tolerate the pain in order to tell what he knows. The doctor returns to the room and asks Jane if he has touched the morphine pump. He says no and then leaves the room.
Jane returns to CBI Headquarters. Cho and Van Pelt have information from Bosco's cell phone records. Apparently, Bosco had been in contact with authorities in another town where a body was found buried in concrete. The radiographs from the body match the ones found in Dr. Morning's office. It is Carter Peaks body, the one that had been missing from the Peak crime scene. Jane realizes that this is a mistake that Red John had made when he killed Carter Peak and therefore removed his body to cover any incriminating evidence. Bosco was apparently following this lead which resulted in his attempted murder and the murder of the other agents. Jane and Cho go to retrieve the body and any other evidence against Red John.
They go the morgue in the town where the body was found. When the doctor opens the locker where the body is supposed to be kept but he finds it empty. He checks the log entries and tells Jane and Cho that the body had already been retrieved by a CBI Agent named Rojo. Jane and Cho realize that it is a fictitious name and that the body and other evidence has probably been disposed of by Red John. Jane tells the doctor to call the technician that released the body so he can describe the individual.
Lisbon is in Minelli's office. He is about to confide in her about something important when Van Pelt enters the office. She has a laptop computer with camera footage from the time around the shootings. It is a picture of an employee that is on maternity leave and could not have been in the picture at the time stamp on the camera. Lisbon remarks that none of the camera footage can be trusted since it has been tampered with.
Jane and Cho question the technician that released the body to the impostor CBI Agent. He describes the person as having olive complexion, wearing a beret in her hair, and walking in high heels that were noisy.
The scene fades to a woman walking in noisy high heels and carrying balloons. It is Rebecca, Bosco's secretary. She is at the hospital and is going to Bosco's hospital room. When she arrives, she greets an unconscious Bosco and approaches his head to whisper in his ear. The scene flashes back to the time of the shootings. Rebecca takes a semi-automatic pistol with silencer from a drawer and places it in a food basket covered with a cloth. She goes to Bosco's office, appears somewhat hesitant, and then proceeds to shoot two agents and Bosco. The scene then returns to the hospital room where she take the same weapon and is about to kill Bosco. Lisbon and Van Pelt arrive, disarm Rebecca, and place her in custody. Bosco wakes from his coma.
Rebecca is returned to CBI Headquarters in shackles where she is placed in an interrogation room with Jane. As they sit facing each other, there is a period of extended silence. Finally, Jane breaks the silence and asks Rebecca what is her favorite kind of music. Rebecca deflects the question and tells Jane that he is wondering how she could do such terrible things for Red John. Jane proceeds to tell her that she had an unhappy childhood, was sexually abused by a close relative, was possibly self-abusive and self-medicating, etc. He continues to profile her psyche and tells her that Red John has filled some dark hole in her emotional needs but that she is really an "object" for his use. She tells Jane that Red John is on a mission of "love" and "enlightenment." Jane tells her that she will one day realize the evil she has done and confess to Jane everything she knows about Red John. She remarks that she will never turn on Red John. The interview ends and she is taken away.
The scene briefly fades to the hospital with Lisbon stopping to talk to the doctor. The action returns to Rebecca being escorted by several security personnel. As she is walking down the corridor, she begins to smile and look at someone approaching that she seems to recognize. As she continues to smile and stare, the individual gets close enough to her to wipe a green gel-like substance on her hand. Within moments she loses consciousness and falls to the floor. Jane hears the commotion and runs to the scene where he finds a dead Rebecca. He sees her hand and the foam in her mouth and realizes that she has been poisoned. Jane angrily pounds the wall with his fist.
Lisbon is in Bosco's hospital room. He confronts her about his prognosis. At first she lies and tells him he will be alright but Bosco's presses her for the truth. She admits that the doctor's don't think he will survive. Bosco then tells Lisbon that he loves her and she replies that she loves him also. Bosco then asks for Jane.
Bosco tells Jane that Red John makes mistakes and that he better capture him. Bosco then asks Jane for a favor. He doesn't want Jane to arrest Red John but to "kill the son of a bitch." To this Jane replies, "that's the plan." He then whispers something into Jane's ear as Lisbon watches through the window. Lisbon rushes into the room just as Bosco dies. She and Jane stand in silence looking at Bosco.
One week later, after Bosco's funeral, Lisbon and Minelli have and emotional farewell since Minelli has decided to retire.
Lisbon enters a room where Jane is sitting on a couch. She asks Jane what Bosco had whispered to him and he tells her that Bosco wants Jane to look out for Lisbon. They prepare to have a shot of tequila (Bosco's favorite) and the scene shifts to another office where Lisbon and Jane have joined the rest of the team. Rigsby leaves the office to get a bottle of scotch and the rest of the team toast to Bosco's memory. Rigsby returns and begins to sing "Amazing Grace." Jane appears preoccupied as the hymn is being sung and leaves the office before it is finished.
In the final scene, Jane opens the box with the Red John files and begins to study the material.