Dan Henshaw urges his toddler, Lilly, to use the toilet. After the appropriate amount of bribery, Lilly makes her way into the bathroom. She lets out a horrified scream when she sees an eyeball and gooey remains in the toilet.
Booth and Brennan tour St. George's Hospital. Brennan wants to have a home birth, but Booth tells her a hospital birth is better. Brennan refutes this theory by shining her ALS light over the floors and walls. There's blood, amniotic fluid, and cerebrospinal fluid everywhere. Now, the other parents on the tour are concerned. Booth gives a sigh of relief when Brennan gets a call from Cam- there's an eyeball in a toilet - they have to go!
At the Henshaw Residence, Brennan and Cam fish remains from the toilet. Tree roots have clogged up the sewer line and remains are showing up in plumbing all over the neighborhood. Was the victim flushed down multiple toilets?
At the Lab, Hodgins pulls bone and tendon from a mass of roots inside a section of sewer pipe. Daisy informs Brennan that she is becoming a certified doula in order to aid the birth, but Brennan's only concern is what Daisy can tell her about the victim. Daisy explains the bone fragments all come from one person. Brennan reconstructs the maxillary sinus to determine that victim is male. She notices the victim has a lens implant. Cam is able to extract it and locate a serial number, which will aid in identifying the body.
Booth and Sweets grab a quick cup of coffee at the diner. Booth asks for Sweets to help convince Brennan to deliver their baby in a hospital. Sweets is touched that Booth acknowledged him as a friend and suggests he and Booth watch soccer and drink beer together. Booth is saved by a call from Angela. She explains that the serial number from the lens implant led to their victim: Rob Lazebnik. He escaped from prison four weeks ago.
At the FBI, Booth questions the victim's wife, Claire Lazebnik. She explains that her husband ripped off his clients in a Ponzi scheme. Lazebnik blew through money with casino trips and yachts. Booth asks if he would have contacted her or anyone else after escaping from prison. Claire explains that Lazebnik burned all his bridges - she doesn't expect to hear from him.
In the Bone Room, Brennan tells Angela that all the bones were fractured post mortem. Cam joins the ladies to inform them the victim wasn't poisoned. Brennan notes there are striations on the ninth rib that could indicate a possible stabbing but she doesn't have enough evidence to make that conclusion. Cam and Angela urge her to "be cool" and call it a stabbing. Brennan can't do it.
Hodgins introduces Daisy to his new toy: a Sewerbot. A motorized car with a camera that will roll through the sewer pipes to see what's inside while Hodgins and Daisy watch via a camera.
Booth brings Brennan to see Sweets at the FBI. Sweets claims he needs to conduct a "Partner Assessment" of Brennan. When Sweets asks a question about giving birth in a hospital, Brennan catches on to their thinly veiled, unethical plan. She yells at them both before storming out.
At the Lab, Hodgins and Daisy see that the Sewerbot has reached gated bars at the end of the line. They realize the sewer ends at Jamestown Federal Prison. Rob Lazebnik never escaped. He was killed in prison and dumped in the sewer.
Booth and Brennan drive to Jamestown Federal Prison. Booth tells Brennan to keep her distance from the inmates. On the drive Brennan proposes a compromise: she will let Booth baptize their baby as long as she can deliver said baby at home. Booth is pleased with the news.
Cam checks in with Daisy in the Bone Room. Daisy can't find any kerf marks on the bones, which means the victim wasn't cut up with a knife or saw. She also found remodeled fracturing on the manubrium, the clavicle, and upper right ribs. It seems Lazebnik was beaten when he was first incarcerated.
Booth and Brennan walk the prison cellblock with Guard Captain, Dave Krinsky. Booth asks about Lazebnik's beating. Krinsky doesn't know who the culprit was but he does know that inmate Haze Jackson stopped the fight.
Angela shows Daisy and Cam her digital reconstruction of the skeleton. Daisy explains Brennan found striations on the ribs, and she found a nick on the L1 vertebra that confirmed the victim was stabbed to death. Lazebnik was doubled over so the weapon hit his inferior vena cava, causing massive internal bleeding.
Booth questions Haze Jackson. He is reluctant to talk since he is being released in two weeks. Booth threatens to change that. Jackson relents, telling Booth the last time he saw Lazebnik he was being summoned to the Warden's Office.
Booth and Brennan pay a visit to Warden Bartzokis. She explains that she found out Lazebnik had been assigned to the prison accounting office. She pulled him off the job, though the damage was done. Funds had gone missing. It was less than five hundred dollars and she nipped it in the bud. Brennan gets a call from Angela. She made a "negative" of the murder weapon and then printed out a positive 3D image of it. The weapon was a shiv.
Brennan searches through the many confiscated shivs at Jamestown Federal Prison. Each one is tagged by the area in which it was found. Brennan finds a match, but it was discovered in the exercise yard. All the convicts had access to the yard. She notes that the weapon was been made from sturdy paper. She carefully pulls it apart to see remnants of writing. Angela should be able to find out where the paper came from.
Sweets checks in on Daisy, who is sitting in Brennan's office, hoping it will clarify things for her. There are no kerf marks at the ends of the bones, meaning the murderer did not dismember the body with a cutting implement. Daisy needs a distraction: the kind that only Sweets can provide. They get hot and heavy on the floor and Daisy accidentally kicks the bones. She rushes to pick them up and notices micro-pitting. The bones were exposed to acid! Sweets' distraction worked!
Krinsky takes Booth and Brennan to the prison's Mailbox Works. Jamestown Prison has worked with the Postal Service since the 50's. Inmates dunk mailboxes in a hydochloric acid bath before painting them. Brennan is going to take acid samples and send them back to the lab while Booth needs a roster of all the Mailbox Works' workers.
Booth questions inmate TeeJay Ouellette, Supervisor of the Mailbox Works. Booth knows Lazebnik once took advantage of Ouellette's parents. Booth gets Ouellette to admit he was the one who beat up Lazebnik when he got to prison. But Ouellette refuses to say any more.
Booth and Brennan finally leave the prison after an exhausting day. Booth believes Ouellette is the killer, but Brennan can't make that assumption. Booth convinces Brennan that she needs to relax. Brennan agrees until she gets a phone call from Hodgins. He tested the acid from the Mailbox Works and it's not a match. There is another type of acid in the prison. Inspired, Brennan rushes back inside.
Brennan and Booth return to the prison. Brennan begins having Braxton-Hicks contractions but brushes them off when she gets a call from Angela. Angela figured out that the shiv was made from a cookbook. Brennan and Booth head for the kitchen.
In the kitchen, Booth finds a drain that is missing screws. It's big enough to dump a body. Brennan locates the cookbook with the missing pages. She grabs cocoa powder to dust for the murderer's prints and sends a picture to Angela.
Daisy visits Hodgins in the Ookey Room. He found synthetic rubber particulates on the bones. It comes from a company that makes shoes for inmates. Daisy realizes that after the bones were immersed in acid, they would be brittle. The murderer stomped on them to get them down the drain. Hodgins adds the last piece of the puzzle: the murderer evaporated vinegar down to acetic acid. This matches the micro-pitting on the bones.
Cam watches Angela pull up the fingerprint results on the Angelatron. They match Haze Jackson, who also works in the kitchen.
Booth and Brennan make their way down the cellblock. Brennan needs to see Haze Jackson's shoes. They should have bone fragments that match the victim. Booth urges Brennan to stop but she makes her way through a sea of prisoners, looking for Jackson. Jackson notices Brennan and starts a prison riot in hope of escaping.
Booth finally reaches Jackson and takes him down before he can hurt Brennan. Jackson admits he killed Lazebnik because he promised to help Haze get financially set up after he was let out of prison, only to find out later, Lazebnik had no money to help him.
They solved the crime but Brennan is in labor!
Booth drives down the road, but Brennan's labor is quickly progressing. They won't make it to a hospital. Booth makes a quick stop at a country inn but the owner doesn't have room for them. He directs them to a building out back.
In a barn filled with animals, Brennan begins to deliver the baby. Booth can't help but point out the similarity between the nativity and their current situation. Brennan admits there is a mystery to life when she finally meets her baby girl.
Booth and Brennan return home to find the whole gang waiting from them with presents and champagne. Booth and Brennan happily introduce Christine Angela to the group. Everyone fusses over the baby, as Booth and Brennan look on, quietly elated about the journey they are about to embark on together.