The episode begins three months later and we see that Brenan is still hiding from the prosecution for a crime she did not commit. She is now, a blonde. Max arrives and tells her that it is time to leave as they have been in this place for too long. At the Jeffersonian, Angela is still trying to figure out how Pelant managed to get Brenan in the footage; she has been at it for months. Hodgins arrives and asks her to take a break. At the office, Booth is frustrated as Flynn doesn’t believe him about Pelant. Booth says that Pelant was at his place and he saw him on the security tapes. But later somehow the computer genius had managed to erase himself from those tapes.
Next, Clark takes over Brenan’s office and asks Angela to make the report on the last week’s murder case, for the binders. Angela is irritated and says that she wouldn’t do that. Cam arrives and tells Angela that if she wants to use this facility to solve Brenan’s case, then she will have to respect Clark. Booth heads to the library where Pelant is teaching computers. Pelant files a case against Booth for stalking. Next, Flynn and Cam arrive at a crime scene. the team received an anonymous tip where in the caller had changed the voice. They are surprised to see that the skeletal remains have been dug up professionally. Angela finds something and declares that Brenan dug up the body and has left a clue for her team. Flynn orders to search the nearby areas.
Brenan has left behind a flower that blooms only in winter. At the Jeffersonian, Angela tells the team that Brenan feels that f they solved this murder, it will clear her name. No one is paying attention to Clark. He then tells them that this remains, is of a woman who has never given birth. Cam instructs that this needs to be relayed to Booth. It is clear that Angela has been secretly communicating with Brenan and she wouldn’t tell anyone how she does that. Just then Booth gets a message saying that the remains belong to a guidance counselor Carol, who went missing 10 years ago. And Booth finds out that Christopher Pelant went to the same high school with Carol.
On the other hand, Pelant watches the news and sees that the decade old crime scene is dug up and he seems a little tensed after he sees the flowers Angela is holding. Booth calls Cam and says that he is going to the Atlantic City. Booth is in a motel and he hears a knock on the door. It is Brenan. They kiss each other. We then see that he is happily playing with his daughter and is excited that he daughter calls him “dada”. She then tells Booth that Max and she looked into Pelant’s background and found that one of the guidance counselors just vanished. Max arrives and tells Brenan that they have to leave. Already? Well, Booth being here changes everything!
At the Jeffersonian, Clark and Cam are trying to figure out the COD; but Clark states that the fracture would only cause impaired motor skills and so the COD is still uncertain. Hodgins arrives and says that the murder weapon was a rock; red agate. Angela tells Caroline that she can clear her name by providing proof that her electronic signature was forged. Caroline is glad. Booth tells Brenan to go through the pictures of the remains and see what she could find in them. Sweets tells Caroline (who is back in action) that Pelant had been suspended for hacking into the school’s computers to change his grades.
Sweets, then tells Caroline that he examined a recommendation letter that the guidance counselor wrote for Pelant and compared it with some of the articles that Pelant wrote. The writing style is exactly the same. Therefore, he wrote the recommendation letter himself and then killed the counselor to cover his tracks. At the Jeffersonian, Angela wants Hodgins to put the flowers in a particular spot. Hodgins reaches the graveyard and finds Pelant waiting for him. Hodgins is furious to see him and he threatens him. But Pelant says that he has read the FBI files and according to the psychology reports, Hodgins is too nice a person to kill somebody. Hodgins throttles Pelant but eventually lets him go. At the office, they discuss the recent events.
One thing is clear that since Pelant has figured out the flower system, Brenan is not going to make anymore drops. Max arrives at the graveyard and says aloud that he is going across the border with Brenan. Max knows that Pelant is nearby and he is right! Hodgins then goes to Sweets and tells him that he choked Pelant till he was unconscious. Hodgins says that Pelant wanted him to do it; he cant explain this but it was written all over Pelant’s face that he wanted Hodgins to kill him. Sweets says that the fact that Pelant wanted Hodgins to kill him, is a valuable piece of information. Next, Max takes Booth’s car and tells him to take his car. Max says that his car is stolen and is untraceable.
So, Booth should take Brenan and Christine in that car. Max knows that Pelant will come after Booth’s car and he will kill him. Booth calls Flynn and tells him that Brenan is trying to escape. he describes the car. Flynn tells him that he is the second person who called in saying that the car is stolen! Actually, the car Booth was driving was Clark’s and Plant discovered that Booth had stolen the car and so Pelant calls in to report the car stolen. At the Jeffersonian, Hodgins tells Cam to leave the office with Clark and the rest of the staff and also take all the security guards with them. The entire facility is empty. Moments later, Booth and Brenan arrive and Brenan gets on to examining the skeletal remains.
And she infers that the victim hit her head on the rock and the wound retracted as she was being pulled to be hung upside down. The victim was gutted and then bled to death. Well, the team missed her so much! At the FBI, Booth hands over the flash drive that Angela gave him, to Flynn. It shows all the incoming and outgoing emails from the Jeffersonian and FBI. Flynn agrees to bring Pelant in. Pelant is teaching in the computer lab and the FBI arrests him. Next, Sweets, Angela and Brenan are trying to decode Ethan’s triangle. Sweets, tells them that Pelant wants one of us to kill him. On hearing this, Angela’s face goes blank. Brenan tells him that this is her thinking face.
Later, Brenan tells Cam that according to Clark’s findings, Pelant used a Japanese sword to kill Carol. Max had coffee with Pelant’s grandfather a couple of times and it appears that the grandfather fought in WWII. They search Pelant’s family house and find a Japanese sword. Next, Pelant is arrested and he smiles as he is being taken. Max says that he would be more satisfied if Pelant was dead. Meanwhile, Angela cracks the code and finds out that Brenan was digitally inserted into the video feed. Everybody is happy. Flynn hands over the office to Booth, Brenan can resume work and Clark joins in to do some serious archaeological work! Booth apologizes to Angela for being angry at her for the past three months.
Next, Booth and Brenan are making out when Booth receives a call. They then arrive at the FBI office where Caroline tells them that Pelant is not Pelant. He is an Egyptian and the Egyptians have arrived to take him home tonight. Booth concludes that Pelant has wiped off his identity and created a new one. On his way out, Pelant hands over a marigold to Brenan. She slaps him. They take Pelant out of the office. Brenan tells Booth that the flower means pain and grief. Booth tosses the flower in the trash can but seconds later it is picked up by Flynn. The episode ends.