While Brennan and Booth are on their way to a crime scene Brennan talks about her vacation which was spent with her brother Russ. She goes on to explain how nice it is to have a brother again and that they both want to find their father whose been missing for years. Brennan wonders why Booth is in such a rush to get to the crime scene.
They arrive to the crime scene to find a derailed train and its path of destruction surrounded by police and emergency medical technicians. Injured passengers stagger about, others aren't lucky enough to be on their feet. Brennan and Booth are greeted by Dr. Camille "Cam" Saroyan. She explains that a car parked on the tracks, probably a suicide, derailed the train.
After Cam bosses Brennan around revealing that she is her new boss at the Jeffersonian. Brennan's not too keen on this idea, but she heads over to the car that caused the wreck to see if she can ID the body inside. She deciphers that the victim was a tall male with an ID bracelet of sorts, but the fire has damaged it. She also notes that the fire damage is too severe have just erupted from the fuel tank of the car. There must have been another catalyst involved. Cam returns to let Brennan and Booth know that they found more dead on the train including a senator.
Back at the Jeffersonian labs Cam is making herself feel at home as she does an autopsy on the dead senator. Brennan and Zack examine the burn victim from the car and confirm that he was 6'7" tall and his shoulder has damage from that of a basketball player. Hodgins looks at the ID bracelet found and discovers that the burn victim is ex-basketball great Warren Lynch, CEO of mega-corporation Lynchpin International. A senator and a tycoon in one accident? Hodgins can't believe it's a coincidence, but then Brennan reveals that Warren Lynch was dead for hours before the train hit him.
The Assistant US Attorney Lisa Supek joins Brennan and Booth at the lab to discuss the findings from the crash site. They present the forensic facts and Booth adds video footage he found taken from a traffic cam earlier that day that puts Lynch in the same vehicle found at the tracks. They note that as soon as the public finds out that Lynch is dead, stock in his company will plummet. Booth thinks that this could be the motive for his murder. Someone could be "shorting the stock."
With this information they bring in Lynch's wife who explains that they were recently separated because Lynch was cheating on her. She found out and to combat her accusations Mr. Lynch hired Rick Turco, a private detective and he found out she was cheating as well. Rick Turco became Lynch's go-to guy for dirty work. Booth knows him by reputation.
Back in the lab Hodgins tells Brennan and Booth that he's found two types of broken glass in the car from the tracks. One type is from the windshield and the other is used for jars. Brennan continues her own examination of Lynch's bones and finds the lack of bone density of someone much older, but all other signs disagree. She comes to the conclusion that Warren Lynch was a heroin addict.
Booth and Brennan meet with the tight-lipped Mr. Turco and threaten to open a drug investigation against him if he doesn't talk. He breaks and reveals that he was actually hired because Warren Lynch was being blackmailed. Turco goes on saying that he negotiated the blackmailer down from one million to a quarter of a million dollars and paid them of just three days prior.
At the lab Cam shares her findings with Brennan in regards to skin samples taken from Lynch's burned body. She found traces of specific opium that had been circulating in the area recently.
Zack drags Brennan away to show her his latest investigative experiment involving a mock skeleton caked with Spam which is set ablaze to show how long the body should have burned for. Their test shows that there must have been another element involve with Lynch's burning because it lasted twice as long. Hodgins also pieced together the shards of the second type of glass he found to form six five-gallon jars, most likely filled with gasoline. Cam arrives to find this blazing Spam circus and lets the team know that all experiments must be authorized by her because she is in charge and wants full control.
Brennan and Booth have lunch and Booth gets a call from the FBI informing him that the man that killed Brennan's mother was just killed in prison. This shakes Brennan to the bone because he's the only man that had any connection to her mother.
Back on the case, Brennan and company surround the Angelator eyeing a composite that Angela put together from Warren Lynch's skull, although it doesn't resemble him in the least. It wasn't Lynch in the car.
Brennan brings Angela to meet with the bullish US attorney and they explain that it wasn't Warren Lynch in the car. Brennan also brings up that they found someone had falsified Lynch's dental records with high-level access and expert skill. This does not impress the attorney.
Brennan and Booth are on a stakeout looking for a known dealer of the specific drug found in the now unknown burn victim's body. They spot him mid-deal and shake him down for information on a 6'7" junkie who he's been dealing to. The dealer says the person they're looking for is Ray. Just then Booth gets a call. Warren Lynch has been found.
At the hospital they are told that Lynch was thrown from a speeding car while already unconscious and sustained major injuries including brain damage. He's probably never going to regain consciousness.
They surround the Angelator as Angela runs a scenario of how Ray the junkie might have gotten his right arm broken because this happen after he died. They concur that he was probably getting forced into a jacket, Lynch's jacket. Angela also double checked the traffic photo taken of Lynch for anything out of the ordinary and she found a reflection off his side window that shows Rick Turco driving in the lane next to Lynch.
Booth brings these new results to Cam and wants her assurance that that Angela will not be penalized for doing research on her own. Cam agrees, but then she and Booth get into it about why Cam took the job at the Jeffersonian. Booth thinks that she took it because of him and their spicy history, but Cam assures him that it was just for the equipment and higher profile cases.
Brennan and Booth take some time off the case and head to a prison to talk to the man that killed the murderer of Brennan's mother. They question him and he reveals that the hit he made was ordered by Brennan's father.
Brennan is shaken and Booth gives her a good talk on the ride back to the lab. He recommends that she seek closure by visiting the grave of her mother.
Brennan thinks this through and reminisces by going through some of her mother possessions. Then it hits her; Lynch was in on the train derailment because the body found had all of his possessions except his most prized, his college championship basketball ring. Booth agrees and they bring in Turco for questioning.
Turco is too good. He knows their questioning procedures and gives nothing up. He has them just where he wants them, until Brennan gets an idea. She tell's Booth to lie and say that Lynch has awaken and confessed. Booth tries this, but Turco doesn't buy it until Brennan uses her knowledge of how the body was handled to convince Turco that what she discovered could only be known by someone that was there. He buys it.
In a meeting with the US attorney, she is happy that Turco has confessed, but he only confessed to helping Lynch load the car. Turco says that Lynch put the car on the tracks, which isn't enough for the US attorney. She wanted to put him away for good on all aspects of the crime. The attorney lays into the lab crew and knocks their sub-par results, but Cam steps up to the plate and knocks right back at her. The crew likes having this kind of protection and Brennan is won over as well.
After the meeting Booth takes Brennan to her mother's grave and urges her to just talk to the headstone. Brennan does so and finds it liberating, then finds something else. She picks up a small silver dolphin from the side of the headstone. Dolphins were her mother's favorite animals. Brennan's father must have left it. He's still out there and he needs closure just like Brennan.