Booth enters Brennan's office to inform her that police think they've discovered the body of Carlie Richardson in the Delaware Bay. She was a pregnant woman who went missing a year prior. Although the case got a lot of press Brennan still has no idea who she is, which spurs an argument between her and Booth about how she needs to get out more. Booth moves on to explain that the story of Richardson. She was a newly wed with a husband that was cheating on her. Evidence on her case says that they had a fight the day she went missing, the husband had scratch marks, and a witness says that they saw him down by the marina.
On the way out of the lab to the bay Booth gets a call from his ex-girlfriend concerning whom their son will spend the weekend with. Booth doesn't like the idea of his ex's new boyfriend moving in on his time with his son. Brennan is losing Zack herself. It seems that Cam has stolen Zack and taken him under her wing. They both head out determined to gets their relationships back.
In the car Booth and Brennan both vent about their issues, Brennan about Cam taking over the Jeffersonian and Booth about the livelihood of his son.
At the scene of the crime Brennan ID's the body as a Caucasian female that has been in the bay for approximately one year. Then she uncovers the fetus, still intact with the female's body. Marks on the bone indicate that the victim was stabbed violently, multiple times. The victim is wearing the same clothes that Carlie was last seen in so Booth exits to go bring in her ex-husband for questioning.
Booth kicks the door down at Kyle Richardson's house to find Karen Tyler, frightened with a bloody nose. She tells Booth that Kyle saw the news about finding Carlie's body, fought with her, hit her in the face, and then left.
Booth arrives back at the lab with a box of evidence from Richardson's house for the squints to examine. The box includes rope, plastic sheeting, and a knife set with one knife missing. The rope is a match. Evidence from the crime seen includes a fish that had been trapped in the plastic wrap with Carlie's body. Zack gives it to a giddy Hodgins who can't wait to examine it. Booth isn't as excited. As he stands over the tattered corpse with the fetal skeleton exposed, Brennan clearly sees that it's affecting him. He storms out, all business, ready to crack this case.
In the FBI interrogation room Booth sits with Karen Tyler who says she was there to comfort Kyle Richardson after the trial. Booth reveals some photos to show that she wasn't the only one comforting him. She already knew about the other women, but swears that he is not the type to murder. She tells Booth that he was planning on divorcing her, but he would never kill her.
At the lab Brennan examines Carlie's bones as Angela stands by. Brennan talks about how she thinks marriage is a fading tradition of the past and is better left there, while Angela assures her that some day Brennan will meet someone that will make everything she just argued sound ridiculous. Zack enters with the skull in fragments and says that the debris in the water has caused a lot of damage. After Brennan asks him to reevaluate the stab markings on the ribs Zack says that Cam has him doing something else. Brennan has to remind Zack that he is studying under her and it's at this time that Cam enters to remind Brennan who's really in charge. She's also found organic tissue underneath Carlie's nails that should match Richardson and has something else to show Brennan in her office.
In Cam's lab she shows Brennan a locket that has melted into the lung during putrefaction. When looked at closely they see that inside the locket an engraving reads, "I love you Kenny." This throws them of the scent because they don't know who Kenny is.
Booth sits at the bar of the diner talking to his son on the phone as Brennan enters to join him. Brennan tries to talk to Booth about his son, but he'd rather discuss the case. Brennan fills him in on locket and Booth can't remember any Kenny in the case file. Booth suggests that they question Carlie's old friends and ask who Kenny might be.
At the park Brennan and Booth talk to Carlie's old friends, Mary Corbis, Faith Davis and Tina Holmes. Booth asks about Kenny only to find out that Kenny was the name of the dog Kyle bought her. The dog has since died. Mary took care of it after Carlie's disappearance. Kyle brought it to her after he "accidentally" hit it with his car because Mary is a vet.
Back at the lab Hodgins show Brennan, Booth, and Cam new discoveries on the trapped fish that Zack gave him. Although Blue Fish is common in the Delaware Bay, he found particles that show that the body was in fresh water for at least six months prior to its time in the bay. Booth chimes in that the witness they have saw Kyle at the bay and with no fresh water around for miles that means that Kyle might not be the murderer.
After discussing the fact that they might have to look for a new suspect Booth follows Hodgins and Brennan to the closest fresh water source that matches the results Hodgins found on the victim. As Brennan dives to the bottom of the lake, Hodgins sifts through sediment and talks to Booth about a woman he once dated that had a child and how hard it was for him. Booth notes that Hodgins is reaching out, but dodges the deeper issue by relying on small talk. Hodgins finds some things that are worth comparing at the lab and Brennan surfaces with bones that might match the fetus.
At the lab Brennan and Zack add the bones of the fetus to the bones found at the lake. All together the fetus would have seven fingers on its left hand and two right hands. When looked at closer she finds that it's a raccoon hand, not a baby's hand. Hodgins enters with the data he's complied and everything he's compared between the body and the lake do not match.
At the FBI offices Booth is briefed on Richardson by another agent. They've found Richardson's plates and car in two different places. Then Carlie's parents come into the room. They have a picture of Carlie and Kyle and in the background is Karen Tyler who said that she met Kyle after Carlie disappeared.
At the lab the squints have recreated Carlie's height, weight, and density in a life size model. The purpose of the model is to see how different sizes of people would stab her. This way they can ID the killer's body type. Kyle Richardson was 200 pounds so Brennan calls Booth.
At the FBI offices Booth agrees to take a stab at taking a stab when his ex-girlfriend comes out of nowhere with a scowl. She begins to chew Booth out for running a background check on her new boyfriend. She threatens to not let Booth see his kid anymore and this puts Booth in check.
Booth arrives at the lab to help conduct the stabbing test. Everyone has a go at it and the matching body type is Angela. Karen Tyler is the same body type as Angela. Angela wonders why Kyle ran if Karen is the killer, to which Cam points out, maybe Karen killed him too and he's yet to be found.
On the bone table Brennan and Hodgins look at Carlie's remains again. Booth stands by. Hodgins notices that there is sediment embedded in the bone from when the knife passed through the body and into the ground. From this he might be able to find the location of the murder. Cam enters to inform the crew that it was Kyle's DNA under Carlie's nails, but he had admitted to fighting with her that day. She also found the DNA of a woman, perhaps Karen Tyler.
Booth brings Karen in for a talk and Brennan takes a swab from her to get her DNA. Tyler denies that she or Kyle would kill Carlie, but neither Brennan nor Booth buys her story.
At the lab Hodgins has uncovered the precise location as to where Carlie was murdered; Gloucester City, New Jersey. No one ever moved the body. The body was dumped in a creek and when heavy rains came six months ago she must have washed out into the bay.
They go to Gloucester, New Jersey to the scene of the crime and uncover an overnight bag that belonged to Carlie. This shows that she wasn't there out of force.
Brennan and Booth go back to the friends of Carlie's and ask them if they know whom Karen Tyler was and Mary the vet says that she saw them together at a Starbucks around the time Carlie went missing. After the visit with the friends and their kids Brennan and Booth have an argument about the worth of having kids.
Brennan and Booth arrive at the lab to find out that the DNA from under Carlie's nails doesn't match Karen Tyler. Also tissue from the fetus showed traces of an anti-depression drug that Carlie was not taking. They reexamine the fetus's skull bones only to find that it's not a fetus at all. This is the skull of a baby that lived at least two weeks. Carlie's fetus was removed and replaced with this baby.
Still in the lab the squints examine the baby's bones to find that it was dead when it replaced the other baby. There is evidence to show that it suffered shaken baby syndrome. Odds are that the mother was on the anti-depression for post partum depression, got upset at the baby, and shook it too hard. The stab wounds on Carlie were all high enough not to harm the child and the marks on the lower ribs must have been from a surgical instrument used when removing the fetus. Booth gets a call; they've found Kyle Richardson.
At the FBI offices Brennan and Booth question Kyle who denies knowing who killed his wife with child. He says that he did want to leave them, but he didn't kill them. They tell him that his child might still be alive.
Booth meets up with Hodgins at the lab where Hodgins explains that he found betadine on Carlie's remains. It's used to keep wounds from infecting during surgeries. Angela has made an aging composite of the baby's skull to help pinpoint who the mother might be. When the Angelator displays the composite Brennan knows exactly who it is.
At the park where Carlie's old friends were questioned Booth and Brennan look for Mary the vet who would have the knowledge and access of equipment to carry out such an act. They find her and confront her and she finally admits to the murder. The baby is taken from her and she's put under arrest.
Back at the FBI offices they present Kyle Richardson with his son. It's hard for him to think of himself as a father, but something almost changes in him instantly that makes you think he might be OK after all.
Brennan and Booth grab a bite to eat at the diner, where they get a visit from Booth's son, his ex and her boyfriend. Booth confronts the new man and as nice as he is Booth can't handle the idea of Parker with a new father figure, but when his ex suggests that maybe they should just leave Booth buckles and realizes that if he's gonna be able to see his kid, then he's gonna have to deal with things the way they are.