Bones had a fight with Booth about parenting moments before leaving for work. The guard-on-duty checked up on her prior to being shot and left moments later to call it a night. Thus, leaving Dr. Brennan alone and vulnerable at the time of the attack.
Anyhoos, a sorry Booth comes to the Jeffersonian to apologize to Bones. Christine in tow, he finds an unconscious Temperance bleeding on the floor of the bones room. As Booth calls for paramedics, Brennan was having a near-death experience and meets her deceased mother.
At the hospital, as Booth and the rest of the paramedics rush her to the ER, Brennan continues her talk with her mom. Brennan, still trying to be logical in her sub-conscious, tells her mother that she is hallucinating, hence, the encounter. Her mother then "explains" that she also could be looking at an alternate reality--heaven. Brennan, declares to her mother her non-belief of heaven and gives her mother a scientific explanation of what's happening to her at the moment. Aaaahhh... Science and religion!
Her mother asks her how her life is now, but Brennan refuses to tell her at first. Considering that she's only a part of her hallucination, she figures that her mother already knows everything about her. But later on, she gives in and spills a bit her life to her mother.
Bones later realizes that she soon needs to go back. But her mother tells her that it's not her call. Frustrated, Bones forces her way out as she tells her mother that she doesn't believe in God. As she finally opens the door, she gets sucked in by a blinding light.
At the operating table, the doctors are trying their best to find the bullet as they found no exit wound. Unfortunately, no bullet has been found and Bones is left on critical state. She then gets sucked back to her alternate reality with her mother.
Still trying to get herself back into consciousness, Bones is desperate to get back to life for Christine. Her mother replies that she once was like that so she can get back to her own daughter (young Temperance), but later on died. Brennan still tries to find explanation on all things and her mother then argues that there are things that are just simply not understandable. Her point: after life.
Cam was one of the doctors at the OR who were trying to operate on Brennan. She meets Seeley at the waiting area to report on Bones' condition. She is relieved to tell Booth that Bones is now stable, though her heart stopped twice and was revived by a defibrillator.
Booth also tells Cam that the guard who was with Bones before the shooting was also killed. He was found dead at the stairwell of the Jeffersonian. They also have no word about the shooter yet. Cam then tells Booth about the puzzle that is the missing bullet. That there is no bullet on Bones' body and that there is also no exit wound on her as well as Hal, the security guard who was also shot dead at the Jeffersonian. Cam demands that Booth should rather stay with Brennan, instead of investigating on Bones' case.
At the Jeffersonian, Hodges, Sweets and Edison sees the aftermath of Brennan's shooting. Sweets could not believe that Bones has survived that massive blood loss and they try to think of who the shooter might be. They have this theory that the shooter could have something to do with the case she's been investigating on. Cam confides on Edison and Hodges about the vanishing bullet on Hal and Bones. And they are now caught into solving Bones' puzzle--er case.
Back at the hospital, Booth sits on Bones' bedside. She is finally awake, but still disoriented. Booth explains to her what has transpired. Bones tells him of her dream. Her father comes in and checks up on her. Booth asks Bones of what she may have seen before being shot. She tells him that it was all a blur, but tells Booth about Hal being there. Sadly, Booth breaks the news to her that he's dead. He also tells her that there was no bullet recovered on either of them.
Being a scientist, Bones knew at the time of her hallucination, she flatlined. She asked Booth how long she was out. He then informed her that she was dead for two minutes.
Back at the institute, Sweets and Sparling (yep she's back) are talking about the investigation. Turns out that all the cameras were disabled at the time of the shooting, so the perp was not ID'd. Their next option: question all the people left at the Jeffersonian at the time of the shooting.
Cam and Hodges are examining Hal's corpse to shed some light on the investigation. Montenegro approaches them happily that Bones is finally conscious, to everyone's relief. Cam though was confused as most gunshot victims would recall that they feel like it's burning at the area they were shot, but Bones feel cold instead. Aha! Maybe that's a clue. Hodges suggests an ice bullet.
As Sweets and Sparling interrogates the people at the Jeffersonian, they found out that Hal was a bit of a klutz. One testifies that he once tasered himself out of clumsiness. Later on, Edison finds out that the victim that Bones was investigating on was killed by a taser. Linking Hal and his taser (that matched weapon on the vic's body) on the murder. Probably the reason why Hal all of a sudden checks in on Bones at that time. Question is: Who shot Hal? And why?
Angela visits Bones. They confer about Hal being the prime suspect on the murder of the vic Bones was working on and that somehow, everything links to one another. Suddenly, Brennan flatlines--AGAIN. She talks to her mother once more and recalls the time her mother died and what happened before that--the fight, the boy, and how they never so each other after that. Her mother tells her that after that fight, Bones became who she is now. A person who'd rather use her brain than her heart and wouldn't change herself for someone. After that, Brennan again comes back to life.
Temperance comes back and she wakes up to Booth, her father and the doctor at the room. The doctor tells her that she had a reaction to the antigens of the blood she had during surgery. Bones tells Seeley her dream. She tells him that it has been Booth the whole time who has helped her come back to life. She confides to him of being in "another place" with her mother.
Back at the lab, Hodges makes his own ice bullets out of water, and demonstrates to Cam how it is impossible to penetrate the human body. Hodges then shows Cam that he had an idea through Bones' blood incompatibility issue at the hospital. He then concludes that the ice bullet used on her and on Hal was indeed made of blood. He made his blood ice bullets and demonstrates how that became the ice bullet that was used on both Bones and Hal. Perfect match. No exit wounds and no bullet trace. Genius. She then comes back into examining Hal's body.
Bones' father brings her her favorite ice cream. He talks to her about Tempe's encounter with her mother. Brennan, instead gives her father a logical, scientific explanation that it was not her mother but just a hallucination. Her father begs to differ and that he thinks that it really was her mother's spirit that she was talking to the whole time. Bones tells him about how her mom misses her father so much and that she still thinks that it was all a dream.
Cam and Hodges discuss about the particulates that she and Clark recovered from Hal's head. Hodges gives her information that the wood shavings that they found were from an ancient tree from Crete dated 12th century with gold flakes. They have the same materials that are of an artifact from their museum that suggests that the perp is also from the Jeffersonian.
Sparling breaks the information with Booth and tells him that the guard called a burner cell before he was shot. Booth thinks that this must belong to the shooter. That the shooter must have shot Bones because she's the only one smart enough to put the pieces together. Another clue that links the shooter to being someone from the Jeffersonian.
As they investigate on the painting, they have noticed that the 12th century artwork is missing and was replaced by a replica. They then realize that this must be a heist-gone-bad. The shooter must have taken the real artwork, replaces it with a fake, gets into a fight with Hal and kills him. Shoots Brennan to stop her from figuring out who the suspect is.
Booth, Hodges and Sparling figures out that the perp is indeed from the Jeffersonian. They come to arrest Dr. Batuhan, the chief of restoration at the Jeffersonian. They see the improvised gun (airbrush compressor) and the cryogenic cooler. Proofs that can pin him as the prime suspect.
At the FBI, Booth and Sparling interrogates Batuhan. He then lets him know that they have already traced some of the missing artifacts and the counterfeits at the Jeffersonian. The questioning has pushed Booth on the edge that he almost assaulted Batuhan at the interrogation. Booth was then texted to come to the hospital as Brennan will be sent to surgery due to some complications from the shooting. Brennan asks Booth to find more evidence to convict Batuhan. Brennan also advices Booth that she'll get those antigens for biopsy to find out if those were Batuhan's.
While on surgery, Temperance sees her mother once more. She notices her mother leaving again as she was "preparing for work". Tempe realizes that she's reliving her last hours with her mom, thinking that after this, she will not see her mother again. Her mother assures her that they'll be together again someday. She leaves Brennan with parting words that "It's time to find that little girl inside you again". That it's not surviving anymore, but flourishing. Brennan, tearing up, tells her mom how much she misses her. Her mom tells Tempe to tell Max that she has always known that the first gift her dad gave her mom was stolen. She then kisses Temperance goodbye, walks out the door as Brennan wakes up to her reality.
Booth smiles as Brennan opens her eyes. He tells her that Batuhan was finally convicted for Hal's murder, and Brennan's attempted murder. Max, relieved stands up and says that he'll be letting Temperance's friends that she has finally awake. But before he walks out, Brennan tells Max about what her mom told her. Max, surprised, informs Brennan that only he knows that. Nobody else has an idea about it until now. This suggests that Brennan may have had a change in her perception about the after life.
***Eugene Byrd reprises his role as Dr. Clark Edison. Ryan O'Neal also returns as Max Keenan, Brennan's father and Brooke Langton as Christine Brennan.
