"The Titan on the Tracks" is episode one of season two of Bones.
This episode opens with Booth and Brennan in a car at night with the lights flashing. Booth was on vacation with her brother; they have decided that they are going to find their father. At the end of the season one finale, "The Woman in Limbo", Brennan got a message on her answering machine from her father, telling her to stop looking for him. Booth says that the FBI is going to find her father; Brennan doesn't want to rely on them.
The Scene of the Crime
The crime scene they are going to is a car crash that is still on fire. The car was hit by a train, and several cars of the train derailed. A bit of a mess, and the bodies are perhaps a bit 'fresher' than usual. The accident is believed to be a suicide. The body in the car is really charcoaled, more than might be expected from a car fire. Brennan also has a new boss, hired whilst she was on holiday, one who knows Booth (who Brennan spends some time testing, and there is a bit of a clash).
The driver of the car was a former basketball player and the head of a company, one of the richest people in the country. He was under investigation and, as a result of this, would have lost everything and spent several years in prison. A motive for suicide, only he had been dead for several hours when the train hit his car. The crash also killed a senator.
Motives for the murder are more than one. If someone shorted a stock, they could make a killing from his death. His wife was separating from him, due to many instances of infidelity, and her deceased husband had employed a private investigator to find dirt on her, presumably to reduce the cost of any divorce. The man was also being blackmailed, and was a heroin addict. Only the dead body is not the man thought. This does not make the U.S. Attorney happy.
The supposed deceased does turn up, but badly beaten with brain damage. So just what is going on? Who was the target? Was the senator deliberately murdered somehow?
In addition, the man who was charged with the murder of Brennan's mother is killed in prison. He was the only connection to Brennan's father.
(Due to PickTV skipping ahead to season four after season one, there was a gap of the best part of two years between me watching the final episode of season one and this one, which didn't help with remembering what was going on.)