"Aliens in a Space Ship" is episode nine of season two of Bones, the forensic drama series based on the books by Kathy Reichs.
This episode opens with Brennan in a dark space with a radio playing. She doesn't seem to know how she got there. She's inside a car and it's the car radio. When Brennan opens a window, dirt comes into the car. Hodgins is in the back seat. He seems to be just coming around and there's something wrong with his legs. Brennan says that he must have got them - the he being the Grave Digger.
Rewind - Back to the Past - The Crime Scene
It then goes back 48 hours. Booth and Brennan are at a crime scene. Some children in the woods found what they think is a flying saucer. There's a window, and inside they say they can see aliens. There are actually two adolescent males inside the 'space ship' (a beer vat), and they've been in there for years. The two were twins who were kidnapped years ago and hadn't been seen since.
The Grave Digger - Serial Kidnapper
The former agent who was in charge of the Grave Digger case advised the parents not to pay the ransom when it was demanded for the two boys. Given that he's a former agent and has a drinking problem, it seems that the case badly affected him. The kidnapper, known as the Grave Digger, had abducted people on six different occasions that they know of. Four families paid the ransom and the victims were returned. The other that didn't was never found either. The kidnapper/killer's method is to bury people alive and, when the ransom is paid, tells the family where the victims are buried and how to dig them up.
Pay the Ransom to Get Your Children Back
The Grave Digger has exactly the same method. He kidnaps children, who never remember the kidnap. It's thought they were stunned. The Grave Digger makes one call, says how much the ransom is and what account to pay it to, and that's it. No other contact; you either pay or you never see the people again. There's a former FBI agent who now works as a kidnap and ransom expert now who has written a book on the Grave Digger, with the help of a journalist. He says he's going to help, even if Booth doesn't like him.
A Wrinkle - Or a Mistake?
However, there is a wrinkle in this case. The father was given 24 hours to raise the money, and he couldn't have done it less, but the twins only had enough air for twelve. Either the Grave Digger miscalculated, because there were two boys, or he never intended them to live in the first place. It seems he only intended to take one boy, but the other arrived and the Grave Digger ran him over. Which means he made a mistake - and mistakes are how people are caught.
Stunned, Kidnapped and Buried in a Car!
Except as Brennan goes to her car, she is stunned from behind. Hodgins runs up behind her and he, too, is hit by a car. The Grave Digger contacts Booth and demands $8 million. This is a lot of money, much than the Grave Digger has ever asked for before. Brennan is wealthy but Hodgins is rich. The fact that Hodgins is the heir to the third largest privately owned company in the country is not widely known, but the Grave Digger apparently knows it. Except that he went after Brennan first and Hodgins interrupted the kidnapping of Brennan by accident, so maybe he found out after the kidnapping.
Brennan and Hodgins are inside the car working out how to survive and see if they can get in contact. Hodgins has a problem, which could kill him. Brennan is going to do something that could help, but will be painful. Outside, Booth is planning to pay the ransom but tells everyone else to keep working the case.
There are two obvious (to the viewer) suspects of the people seen and two less obvious ones. Especially as the Grave Digger targeted Brennan after she started investigating the case.
Brennan compares the Grave Digger to God and provides her reasons. Booth does not like the comparison.
Not a cliff-hanger ending, but some things are not resolved at the end of the episode.