At a bar, downing his sorrows, Booth confides to former priest and current bartender and friend Aldo Clemens that he lied to the woman he loves. He asks Aldo if there’s somewhere more private where they could talk.
In a walk-in fridge, Booth reveals all to Aldo about Pelant and the real reason why he called off his engagement to Bones. At first Aldo suggests to Booth that he tell the truth to Bones. Booth balks and tells him that he needs to kill Pelant instead. Aldo agrees that is the only solution.
Back at the office, Dr. Sweets and Caroline give Booth a hard time for canceling his proposal to Bones. Booth dodges their questions and they are soon interrupted by a text about a dead body found at the Lightfoot Hotel.
Booth meets up with Bones and Booth at the hotel’s crime scene where there is a set of remains inside an air conditioning unit. They come up with the scenario that the victim jumped from their room and was dragged. Cam tells Booth that if he doesn’t warm up his cold feet then he will lose Bones forever. Booth tells her to mind her own business.
Sweets introduces Booth to the hotel’s manager, who tells him there are no video cameras because it’s the kind of hotel where men bring ladies who aren’t their wives. The manager tells Sweets and Booth that there is a guest who was scheduled to check out that day but who has not.
Booth and Bones meet in the hotel room of the missing guest. They discover that someone other than the cleaning staff has cleaned the room. Bones is upset that Booth didn't answer his cell phone or come home the night before. Booth states that he was working, but she knows he is lying. Booth tells her that he loves her and that he would die for her. Bones finds smears of blood that someone cleaned up using vodka. They designate the crime as a crime of passion.
Hodgins and Daisy are in the air conditioning unit that’s been brought over to the lab and they discover a wristwatch.
Bones tells Angela that the victim has been identified as Jonas Seidel, an accountant with the State Department. Bones wants to get back to the lab and suggests that Booth bring Dr. Sweets along with him to the State Department.
At the State Department, Booth and Sweets meet with Jonas’ boss, Mr. Norman. There, Booth receives a call from Angela who tells him that someone at the office texted Seidel numerous times before his death. Booth has Angela call the number, and the receptionist, Lily, receives the call on her cell phone. Booth tells her that he needs to bring her in for questioning.
Booth questions Lily, alongside her lawyer, who happens to be her mother. Lily tells him that she did not have sexual relations with Jonas nor did she kill him and she hopes that he finds out who did.
At the lab, Bones receives a text from Booth about grabbing a late lunch. Cam and Hodgins tell her to go.
Booth and Bones have lunch. Booth brings up Christine and Bones tells him that it feels like he’s not there for them. They discuss the case. Booth tells her that he thinks Lily wants to tell him the truth. Bones tell him that the truth is best. Booth tries to reassure her that everything will be okay, but Bones is having trouble believing him.
Hodgins and Daisy rig up a giant parachute apparatus to the fan to remove the rest of the remains.
Booth and Sweets arrive at the victim’s apartment. Sweets is attacked by an assailant who flees out the window.
Booth chases him into a parking lot filled with school buses. The assailant has a gun, and Booth ambushes him. Before any actual violence happens, he greets the mystery man by name: Danny Beck. Danny is an army buddy of Booth's who is now a CIA agent. Danny flees and Booth lets him, much to Sweets’ dismay.
Booth reveals to Sweets and Caroline that Jonas Seidel was a CIA operative. Danny's job is to "sanitize" the apartment. Caroline is dismayed that the CIA won’t help the FBI out, but Booth says the CIA can work from their side and that the FBI can work from theirs.
At the lab, Cam and Hodgins discover the cause of death is an abrasion, or as Hodgins says, a boo-boo.
As Angela and Booth are discussing the case, Booth tells Angela to stop telling Bone that he’s lying to her. Angela tells him that he is breaking Bones’ fragile heart.
Booth visits Aldo again for some counsel. He says to him if he will kill Call for Bones, why hasn’t he Pelant? Aldo asks him how will Bones feel once she learns Booth has put her happiness ahead of the lives of five innocent people, how will she react? He says that Booth always knew the answer.
Angela and Hodgins discuss Booth and Hodgins mentions to her that he thinks there is something going on with Booth that they don’t know about. Angela wants to recreate the last image printed on the victim's computer, which is called "ghosting."
Bones and Daisy determine the cause of death was two blows to the head.
Angela reveals that the last picture that was printed was of a couple in bed at the hotel. Bones spots the initials on the briefcase in the room and that it belongs to one H. Gloeckner.
H. Gloeckner is Heinrich Gloeckner, a German businessman. He identifies for Booth and Sweets Lily's picture as a woman called Melody and Jonas called himself John. Jonas was blackmailing him to use a certain team of consultants for a Chinese dam project. Gloeckner says he suspects the two were CIA agents.
Bones, Angela, and Daisy go out for dinner. Bones asks Angela about her relationship with Hodgins in an attempt to understand her own relationship with Booth and why it’s failing. Bones tells the women that she suspects Booth is going to a strip club because she’s found match books advertising “Paradise Lost” in his pockets.
Booth and Caroline meet with Lily and her lawyer (mother). Lily agrees to help with their investigation even though her mother disapproves. Once her mother leaves the room, Lily reveals that she was recruited by Jonas Seidel for the operation. She also tells them that her mother happened to be at the bar that night and mistook her for an escort, rather than an agent.
Cam tells Bones to not give up on Booth because they are both miserable without each other, therefore they are still madly in love with each other. Bones tells Cam the deceased was struck with something made of leather that caused the bruise. Cam tells her to pass the new information along to Booth.
Booth and Bones confront Lily’s mother about how she hit Seidel with her briefcase, when she wrongfully believed was her daughter's pimp, and they place her under arrest.
Bones shows up at Paradise Lost, which happens to be the bar where Aldo works. Aldo asks if she’s “Booth’s girl.” Aldo tells her that he was Booth's confessor when he was a sniper and confessed to him whenever he killed someone. He also tells her that Booth loves her, and that she should have faith in him.
It turns out the mother/lawyer is innocent. Bones, Booth, and Angela wonder who could have killed Jonas. Booth suggests that Lily’s boss seemed very protective of her. Angela asks if he carries a cane that could have caused two blows to the head.
Bones and Booth return to the State Department. Mr. Norman confesses to the crime. He thought Lily was in danger.
Danny meets with Booth and tells him they owe him one. Danny offers him a job at the CIA. Booth considers it.
Booth returns home to Bones. He tells her that Danny confessed to dumping the body into the air conditioner to avoid anyone identifying the body. Bones tells him that she trusts him and she loves him. But, she says, the next time, it’s his turn to ask her to marry him.