Brennan, Cam, and Hodgins examine a body on the platform in the Jeffersonian lab. Preliminary examination implies the man died from either jumping or being pushed of a bridge. Cam, after seeing some evidence of a heart attack, wants to examine more of the tissue. Seeing as how the body will be tied up during Cam's tests, Brennan decides to return home to put her Christine to bed.
At home Booth and Brennan feed Christine. Booth would like to take Christine out to a ball game but Brennan doesn't think that would be a good idea. Booth gets angry that Brennan wants to rationalize everything and can't simply live in the moment. Brennan thinks Booth is implying she is a bad mother and storms out, heading back to the lab.
Brennan works alone in the bone room, looking at the now clean bones. She is arguing with herself concerning her recent fight with Booth. Hal, a security guard who is surprised to see her working so late, interrupts her. He asks how long she is going to be working, and then inquires about the body. Brennan explains that further examination of the body revealed that he was in fact murdered first, and then thrown from a bridge to obscure that fact. Hal leaves Brennan to do her work. Brennan ignores phone calls from Booth and continues to power through her examination. Brennan puts on her magnification visor so she can better examine the bones. Shortly thereafter footsteps signal the arrival of who Brennan believes is Hal, but of course she can't tell because the magnification of the visor distorts her vision. She looks up to explain that she is too busy to socialize when she is shot, and falls to the ground.
Booth arrives later with Christine. He is mid apology when he steps into the bone room and finds Brennan barely conscious on the floor. Booth immediately calls an ambulance and tries to keep her awake.
A flash of light comes and takes a now conscious Brennan to a brightly lit living room. A kindly woman approaches and embraces Brennan. Brennan is shocked to find she is being greeted by her long deceased mother.
Booth rushes through a hospital corridor along side several medics who are pushing Brennan on a gurney. He argues with them asking about her condition. Hearing that she has lost a lot of blood he leans into her face and tells her to fight.
Another flash of light takes us back to Brennan in the living room. Brennan identifies her situation and determines that she is hallucinating. Her mother tries to convince her that this is real but Brennan won't buy it. She wanders around the room. It looks exactly as she remembered growing up.
Brennan's mother asks about her life, and Brennan talks about Booth and Christine. Brennan wants to leave and get back to her family. She tries to open the door but it won't open. She fights to pull it open, and is sucked into a bright white light.
In surgery - doctors, including Cam, operate on Brennan. They are confused because they cannot find a bullet. They also can't find an exit wound. Brennan's heart stops. They charge the defibrillator and begin trying to shock Brennan's heart. Cam looks on with worry hoping that her friend won't end up on her autopsy table.
With a flash of light, Brennan is back in the living room. She is confused to find herself back in the house and wearing the same clothes that she was wearing when her mother abandoned her as a child. Brennan looks for another exit as her mother tries to calmly explain that the decision to return to real life is not Brennan's to make. Brennan doesn't understand, and her mother responds that some things are simply not understandable.
Cam finds Booth in the waiting room. With a hug she tells him that Brennan is stable though her heart stopped twice during the operation. It's a miracle that Booth decided to go the lab when he did and had he been five minutes later Brennan wouldn't have made it. Cam asks about the shooter, and Booth tells her there is nothing new. Hal was also found dead. Cam wants to return to the lab and autopsy Hal and see if they kind find a bullet in him, because they were unable to find one in Brennan.
Back at the lab, Hodgins, Sweets, and Clark watch as crime scene investigators take pictures. Clark is going to step in and finish what Brennan was working on. Cam arrives and tells the group that they were unable to find a bullet in Hal. Nothing seems to add up.
Brennan comes to in her hospital bed. Booth jumps up from his chair to comfort her. Brennan mumbles that she was cold at the wound site when she was shot. Max arrives relieved to see his daughter awake and speaking. Booth tells her that there was no bullet and Brennan tries to help but Max and Booth keep her down. They tell her she was dead for a full two minutes.
Sweets and Agent Sparling pace the cat walk and discuss the investigation. The security cameras had all been disabled and Hal's badge had been used to access the lab. They're hoping that interviewing one of the techs will shed some light on the case.
Angela comes into the autopsy room and informs both Cam and Hodgins that Brennan is awake. Cam is examining Hal's body for clues. They discuss the fact that Brennan felt cold at the wound site, which is strange as bullet wounds are normally associated with a burning sensation. Hodgins posits that perhaps the killer used a "ice bullet"; something which, until now, has only existed in theory. Cam tells Hodgins to set up the test.
Sweets and Sparling interview several suspects. Among the facts that are revealed we find that Hal was a new security guard and a bit clumsy. So much so that he once accidently fired his taser into the floor. After the interviews Sweet and Sparling sit in frustrated. Sweets thinks everyone looks guilty, and Sparling comforts him.
At the hospital Sweets updates Booth on their findings, or lack thereof. Booth is upset they haven't made more progress but he is more upset that the last words he spoke to Brennan before she got shot were spoken in anger.
On the lab platform, Clark finds that a couple of puncture wounds on the bones Brennan had been working on. They correlate with Hal the security guards taser. Angela arrives with the identification of the body: Johannes Groot. It would appear that Hal killed Johannes. It explains why Hal was sp interested in the body Brennan was working on and how the security cameras got shut off. But who killed Hal?
Sweets and Sparling examine Johannes Groot's apartment. Sweets sees a few things that don't add up. An antique clock worth ten thousand dollars sticks out in an otherwise normal apartment. They discuss their failed an attempt at a relationship and Sweets apologizes for not having called after their previous dalliance. Further investigation shows more cases of extravagant spending beyond Groot's means as well as damage to a coffee table. Around the coffee table are little flecks of confetti with numbers printed on them.
Angela visits Brennan in her hospital room. Angela tells Brennan that when you fire a taser it releases little bits of confetti which identify it. The confetti found at Groot's apartment matches Hal's taser. So it would appear that Hal tased Groot, and Groot's heart gave out. Brennan's heart monitor signals an alarm and Brennan passes out.
A flash of light brings us back to the living room with Brennan and her mother. They talk and drink tea. She speaks about the last time they had spoken. Brennan and her mother had had a fight back then. Brennan's mother thought she was changing herself too much for a boy, changing her clothes and taking up smoking. She had told Brennan she was too dreamy and emotional, making decisions based on what she felt rather than using her brain. And when she had tried to comfort Brennan, Brennan slapped her hand away. Brennan has carried the guilt of that moment, slapping her hand away, ever since. Her mother smiles and says that's why Brennan so strictly adhered to that last bit of advice. Never changing herself and succumbing to emotion. Brennan hugs her mother and disappears in her arms.
Brennan comes to in her hospital bed. Max and Booth stand over her thanking god that she's ok. A doctor comes in and tells them Brennan had a reaction to the blood they gave her. It doesn't make any sense because the blood they gave her matched perfectly - there shouldn't have been any negative effects. After Max and the doctor leave Brennan tells Booth that she has been going to "another place" where she is speaking with her mother. Brennan says she is hallucinating but Booth thinks that Brennan is actually seeing her mother. Brennan goes back to sleep and Booth kisses her forehead.
In the lab Hodgins has put together an ice bullet. He demonstrates one for Cam while explaining all the problems he has had trying to get it to work. When Cam claims it's impossible Hodgins replies only if you define an ice bullet as frozen water, and a gun "as a gun". Using a C02 propulsion cannon and frozen centrifuged blood he is able to get the desired result. The reaction Brennan had in the hospital was not to the blood transfusion, but to the blood that comprised the bullet.
In autopsy Clark tells Cam that he found a small cranial fracture on the left side of Hal's body. They shave the head and find a small wound behind the ear. They cut through the wound and collect puss and particulates for further examination. The particulates seem to be flecks of wood and something shiny, maybe gold.
In her hospital bed Brennan examines her x-rays. Max tries to get her to calm down and rest, and brings her some ice cream. Brennan and Max talk about Brennan's "hallucinations." Brennan says that her mother asked after him. They reminisce and talk about how happy they used to be.
Hodgins arrives in autopsy and tells Cam that the paint and wood found in the Hal's wound were old. Carbon dating revealed over five hundred years old, and the flecks were gold paint. They determine they must be from an artifact of some kind and that there is an artifact at the Jeffersonian that matches those specifications. It is incredibly rare and very valuable. Cam asks Hodgins to have the antiquities' department check for any missing artifacts or forgeries.
Sparling and Booth walk through the hospital as Sparling updates Booth on the case. The guard's last call was placed to a burner cell, which must belong to the shooter. The conclusion being that Groot, Hal, and the shooter were all working together. The shooter must have shot Bones because he thought she was the only one smart enough to figure it all out. They also figure that the time differential between when Hal made the call, and when Brennan was shot, is short enough such that the killer must have already been in the Jeffersonian.
On the lab platform, Hodgins, Angela, Cam, and Booth look at the artifact that matched the particulates found in Hals' head wound. Booth sees that it doesn't look damaged in any way and that is because it is a forgery. A small paintbrush hair found stuck in the paint is comprised of the fur found on a North American squirrel (something not too common in Crete 500 years ago when the artifact was supposedly created).
Sparling, Hodgins, and Booth go to the art department where we find Dr. Batuhan who is the only one at the Jeffersonian capable of creating such a perfect forgery. We recognize him from the earlier montage when Dr Sweets and Sparling were interviewing the members of the Jeffersonian staff who were working at the time of the shooting. Dr. Batuhan is sitting at his desk working on the very same artifact whose forgery we saw in the previous scene. Hodgins takes a sample of it with tweezers and sits at a microscope, matches it to the artifact used to strike Hal the guard. He also finds a cryogenic device that, while rarely used in art restoration, would be perfect for freezing a blood bullet. Booth spots a hollow tube that could be used as firing tube. He rigs it to a can of compressed air and fires a pencil which sticks into a wall. They arrest the doctor.
In the interrogation room Booth and Sparling talk to the doctor and his lawyer. They reveal that they have found several forgeries in the storage room, and several incidents of missing paperwork. They lay out how the crime would have been committed. Dr. Batuhan would slip out of the lab and give the artifacts to Groot, and together they would fly on his private jets to the buyers. Booth gets a call and slips out, while Sparling pulls out several folders to continue questioning the Doctor. They have to hold him while Booth finds more evidence otherwise they won't be able to charge him.
Booth arrives at the hospital just as Brennan is being wheeled out to surgery. Brennan believes that the blood bullet struck one of her bones leaving antigens. She is willfully undergoing surgery to recover them so they can be used as evidence. It is very risky, but she tells Booth its risk free to soothe his nerves.
Brennan is wheeled into an operating room with several doctors, including Cam. She is put under anesthetic.
One final flash of light takes us back to the living room. Brennan's mother is packing. She claims that she is just going to work but Brennan knows this will be their last opportunity to talk. Her mother tells her to ignore the advice that she gave her way back when. Using only her brain was necessary for survival but now it was time to find that little girl she had locked away. Now it's no longer about surviving, it's about flourishing. As they bid each other farewell her mother tells Brennan to tell Max that that she always knew the first gift Max gave her was stolen. And with that she opens the door and walks away.
Brennan comes to in her hospital bed and looks up at a smiling Booth. Max is sitting in the corner. The procedure was a success, the blood matched, and Doctor Batuhan was convicted of murder. As Max leaves to grab the rest of the gang, Brennan tells him that her mother knew his first gift was stolen. He claims no one could have known that, no one but him. He walks out somewhat confused. Brennan comes to grips with the fact that it wasn't a hallucination, and that she had in fact seen her mother. Booth and Brennan embrace each other.