Two guys sit on a sandy beach at the Chesapeake Bay Pier. It's a perfect morning, but unfortunately they have global warming to worry about. If that weren't bad enough, there's also pollution. They notice a plastic soda can holder floating in the water. One of them pulls it out but there is something else attached: the top half of a skeleton. They both recoil in fear.
Sweets, Booth and Brennan sit in Sweets' office in silence. Booth plays with a slinky. Brennan stares into space. Sweets waits patiently. Booth puts the slinky down. His phone vibrates. "Thank God somebody got murdered." Booth and Brennan jump out of their seats and run out the door.
At the Chesapeake Bay Pier, Booth and Brennan meet Cam and VINCENT NIGEL-MURRAY, one of Brennan's grad students. As one of her smarter pupils, he is ready to assist in any way. However, Brennan wants Mr. Nigel-Murray at the lab. Vincent believes he can be useful in the field. "I need a forensic anthropologist in the lab so I can spend my time aiming Agent Booth in the right direction." She gives Vincent the keys to her car. He leaves.
The skeleton waits on a tarp near the water. Cam, Brennan and Booth approach. Without the lower half, Brennan cannot determine gender. There is no pelvic bone. Cam infers that the victim is female due to the remains of a blue bathing suit. She also believes that the victim has been dead two to three weeks. In addition to a severed spine, there is trauma to the fingers, which suggest foul play. Cam notices a possible breast implant. The serial number can help identify the victim. Their next move? Find the lower half of the skeleton somewhere in the ocean. This won't be a day at the beach.
At the lab, Cam and Vincent work with the remains. Vincent reports that the eye sockets have been ground down. This is most likely due to plastic surgery. Hodgins appears. "The victim died in the same body of water in which she was found. Probably within six miles." He doesn't hold much hope for the new intern. Case in point: Brennan addresses him as "Mr." Nigel-Murray, which is a way of saying he isn't a doctor. Vincent ignores Hodgins and continues to rattle off random trivia. As Cam tries to keep Vincent on track, a Jeffersonian employee gives her a file. "The FBI's traced the breast implant to a Baltimore plastic surgeon. He replaced a leaking implant for this woman."
Brennan and Booth drive to Maylor Island, Maryland, a small town with a few thousand inhabitants. They discuss the victim: PATRICIA LUDMULLER. She went for a swim one morning and never returned. Brennan notices that Patricia has very stunning features. Booth reminds her of the plastic surgery. Brennan is puzzled. "Why go to this much trouble to make yourself look beautiful and then move to the end of the world?" Five years ago, Patricia didn't exist. She must've been in hiding.
Brennan and Booth inspect Patricia Ludmuller's cottage. Brennan sees notes for a sermon and a photograph of her dressed in robes with a congregation. Patricia was a Pastor. Booth is surprised that a pastor would be so vain. She had breast implants, veneers and other plastic surgery. "The Pope sits on a throne. He wears robes worth thousands of dollars. Isn't that vanity?" Brennan argues. There is a message on the answering machine. JP needs to see "Pattie." Booth gets a call of his own. The other half of the skeleton has been located.
Cam and Vincent conduct an examination of the lower half of the body. Vincent reports that the lower half begins where the top half left off. It's a match. The victim was dead before he was cut in two. Cam is confused. According to Vincent and the pelvic bone, the victim is male. According to Cam and the vagina, the victim is female. "We have one victim with two sexes."
In Booth's office, Booth and Brennan sit with Sweets. The victim was transgender. Booth suggests that someone from her congregation could've killed her after finding out she used to be a man. Or perhaps it was the man on the answering machine. If he later found out Patricia had been a man, he could have been angry enough to commit murder. Booth doesn't believe that JP knew Patricia was a man. That was an "ain't too proud to beg" phone call. Sweets offers that perhaps something happened when Patricia was still a man that got her killed. Booth is in the process of trying to discover the victim's prior identity.
Brennan and Booth join a gathering on the beach to honor Patricia. WADE SCHMIDT speaks about the leader, pastor and person Patricia was. She brought them together. They all drop their heads to pray, including Booth. After the ceremony, Booth and Brennan approach Wade. He knows they are from the FBI and calls to CHUCK KENNEDY. Chuck, in a wheelchair, approaches. He is not pleased to see them. He believes Patricia's death was accidental and that the investigation will only serve to place blame on the colorful members of their church. Chuck leaves and Wade explains that he is grieving. Booth asks if he knows JP. Wade points to a man standing near the water, staring off into the sea.
Booth questions JP at the FBI with help from Angela in the observation room. JP joined the Inclusion Church six months ago, after a two-year stint in jail. "I had a drinking problem which gave me problems with the law, which gave me marital problems." He thought the church could help him rebuild his life with his wife, RITA GRATTON. She doesn't exactly trust him right now. Booth plays the message he left on Patricia's answering machine. JP claims he was only calling for counsel about his wife. Angela picks up a photograph from her file in which Patricia and JP stare at each other lovingly. "He knew that she used to be a man," Angela realizes. JP admits that he did know but he didn't care. He had feelings for Patricia.
At the lab, Cam, Brennan and Vincent stand over the cleaned bones. The tox screen shows evidence of hormone replacement therapy as well as several vaccinations, all of which are required to travel to the Far East. "Did you know that only 20 percent of Americans have passports?" Vincent offers. He tries to make the tangent seem relevant by suggesting that the victim had her sexual reassignment surgery in another country.
Vincent sits with Hodgins, who is quite annoyed by his presence. Vincent wonders about Zack and Hodgins doesn't sugarcoat it. "He joined forces with a serial killer who was the last in a long line of cannibalistic murderers specializing in knocking off members of secret societies and building skeletons out of their body parts." Vincent is a bit taken aback. Angela approaches. Vincent attempts to woo her though he fails miserably. Angela shows her sketches to Hodgins. She made Patricia look more masculine in an effort to determine her identity before the operation. Vincent and Hodgins recognize the face...
Vincent, Hodgins, Cam and Angela watch a video of PASTOR PATRICK STEPHENSON. He preaches to a crowd and begins to throw his money around the church because it doesn't belong to him. It belongs to God. He encourages the parishioners to do the same. At the end of the video, Patrick is joined by his wife and son.
Booth and Brennan speak with Patrick's wife, CECILIA STEPHENSON, in the FBI conference room. She believes that her husband was robbed and killed on their World Tour six years ago and is certain Patrick would not have a sex change. "He would never offend God in this blatant manner." Brennan tells her that DNA confirms it: the woman they found is Patrick. They believe he took $25,000 from the church for the operation. Booth shows Cecilia canceled checks: each month Patricia sent a check to the church. They assume she was repaying the money. Booth wants to speak to RYAN STEPHENSON, her son, but Cecilia isn't sure where he is. After Patrick disappeared, Ryan left the church. Cecilia can only think of one person that may have committed the murder: ARTHUR FORD. Arthur's son gave every penny of his trust fund to the church. Arthur was not pleased, but according to Cecilia "the Lord touched him." Booth is intrigued. "How much money did the Lord touch him for?"
In the car, Booth discovers that Arthur's son donated five million dollars to the church. However, Arthur died three years ago. They are back to square one. Brennan wonders if Cecilia truly loved Patrick. Booth doesn't think so. "Would you like me just as much if I were a man?" Booth jokes that he would like Brennan more. What if Booth were a woman? Brennan hesitates but the truth is "I'd be jealous that you might be prettier than I am." That's a valid concern. "I'd be hot," promises Booth.
Sweets, Brennan and Booth discuss how to locate Ryan Stephenson. Booth believes they should begin their search in California, his last known location. "This kid, he's the Prodigal Son. I'll bet he's within 20 miles of that giant church he fled as a confused adolescent," Sweets tells him. Booth wants to make it interesting with a wager. They each give Brennan $20 to hold.
At the lab, Vincent explains that Patricia drowned. The blows to the head and pelvis didn't kill her. They were inflicted while she was alive. In both wounds, Hodgins found fiberglass and resin. She was most likely hit with a boat but what caused the damage to her fingers is still a mystery.
At the FBI, Ryan Stephenson a heavily tattooed young man with piercings and black hair sits in the interrogation room. Booth located Ryan but Sweets won the $20. Ryan was in nearby Silver Springs at a detox clinic, not as a patient but as a counselor. He takes the news about his father well, especially when he hears that she opened a church that included everyone. His only regret is that he never knew Patricia. In fact, he now loves his father more. "He didn't want to shake my faith. He was sparing me the truth. He didn't want me to have to choose between him and God." He asks for his father's bible when the case has been closed.
Brennan joins Cam, Vincent and Hodgins at the lab. Together, they determine what happened during the last moments of Patricia's life. She was hit by a boat, the first time in the head. Then the driver turned around to finish the job. Patricia reached up for help but the murderer smashed her fingers and ran her over again.
Cam readies to leave the lab for the night when Vincent approaches her. He wonders if she can help him. He'd like to quit. Everyone at the lab has such a narrow focus. Their styles are completely different, and as a lover of knowledge, Vincent doesn't see this as a good fit. Cam assures him she will fix things so he won't lose his academic standing. He leaves her with one last tidbit. "Did you know that over of people will respond with thank you if you say you're welcome?"
Brennan and Booth drive to Maylor Island. Angela and Hodgins have told them exactly what kind of boats they are looking for: a Lee Shore Island or a Bow Wave runabout. According to a variety of factors such as size and wood-grain, one of these models was used to kill Patricia. Booth wonders how her body ended up in two pieces. Brennan tells him it was caught in a fishing line that severed the spinal column. In life and death she was split in two.
The FBI searches the boats on the Maylor Island Marina. As the community looks on, they single out one boat: it belongs to JP. JP and his wife, Rita, follow Booth and Brennan to the boat. Rita listens as they accuse JP of killing her. JP denies everything. He and Patricia were in love. Hodgins finds the object used to smash Patricia's fingers: a fire extinguisher. Booth sits in the boat. He can barely fit. JP says he restored the boat for his wife. Patricia wanted him to do something for someone he loved. "Then you should have built it for her," Rita says. She has heard enough about Patricia. Rita waited for her husband through the alcohol, his jail time and the church. Patricia was the last straw. Booth places Rita under arrest.
At the Inclusion Church, Ryan Stephenson, the new pastor, gives a sermon. He reminds the congregation that though they may appear different, they are all alike inside, where it counts. He hopes he can come to know his father, Patricia, though each member of the community. Brennan and Booth sit in the crowd, listening to the sermon. Booth is touched though Brennan disagrees with the notion that they are all the same inside. What does she believe? "I believe in always swimming with a buddy."