The past and present collide when human remains from a 150-year-old slave ship, the Amalia Rose, surface. The team is tasked to give the deceased a proper burial but make an unforeseen discovery linked to a recent murder. In the course of the investigation, Booth and Brennan are led to a different kind of ship - a "Cougar" cruise - where they learn their victim was seen moments before his death. Meanwhile, Sweets struggles to maintain a casual relationship with Daisy, and Cam discovers a surprising and emotional connection to the Amalia Rose.
- Booth (David Boreanaz) wakes up from a deep sleep, cracks seemingly every bone in his body and answers his front door. It's Bones (Emily Deschanel), who reminds her partner that he must get his "fitness for duty" report from Sweets (John Francis Daley). The two head to work -- and find Sweets and Daisy (Carla Gallo) naked on latter's couch! "Sign this," says Booth, handing the psychiatrist his fitness forms. Embarrassed, Sweets immediately signs. Problem solved.
Later, the team receives a number of skeletons from an ancient slave ship recently recovered from the ocean floor. Their charge: identify the remains. One of the skulls has a "pink slime" on it. "Something is very wrong," Bones says. "Given the condition of his cartilage, this man dies less than a month ago ... this is murder." Further investigation reveals the victim was less than 20 years old -- and might have been the recipient of long-term physical abuse. Sweets, meanwhile, complains to Booth that he can't keep his hands off Daisy -- despite the fact the two broke up. Booth has little sympathy.
Angela (Michaela Conlin) then runs a facial reconstruction program on the victim, who the team theorizes was dumped in the ocean and got caught in the slave ship's old fishing net. Booth runs the face through the FBI database and comes up with a name: Mike Casper (Jeffrey Johnson). There's only one problem. Casper is 28 years old with a family. Bones insists they have the wrong name. Booth insists they have the right one. It turns out Bones is correct. Casper is very much alive. His identity has been stolen, however. "That piece of dirt cost us the house we were going to buy," Casper says. His wife, Claire (Kerry O'Malley), agrees.
Later, Bones explains that the victim showed signs of repeated blows to the face between the ages of two and 14. She suggests Angela might "de-age" the victim in her facial reconstruction program. It works! The new reconstruction is a 97-percent match with a boy, Liam (Griffin Cleveland), who went missing 10 years ago. Hodgins then enters the lab with news: the pink substance is also known as the "bone-eating snot flower." He demonstrates how the organism works with a cannoli and a straw. It's gross, but effective.
B&B and Sweets then head to a dock where they know a former foster home friend of Liam's works. The young man's name is Hunter (Paul James). Turns out Liam testified against Hunter, a partner in many petty thefts, to reduce his own sentence. So, Hunter has motive. He also has a fun job: working on a "Cougar Cruise," which is exactly what it sounds like. So Booth, Bones and Sweets step aboard to find older ladies dancing with younger men. "It's all just wrong," Booth says. Sweets gets plenty of attention -- and so does Bones!
Sweets, a former foster child, then approaches Hunter, cruise bartender. Hunter admits Liam hurt him by testifying, but the two had patched things up. He also explains how Liam would come on the Cougar Cruises to get money from the ladies. He was especially friendly with cruise-director Nadia. Back at the lab, Hodgins (T.J. Thyne) adds piranha to a pool containing the bones covered in pink-fuzz flowers. The fish eat the bones clean, revealing a series of abrasions. "Doesn't it look like somebody attacked our dead guy with a grater?" Hodgins asks. Sure does.
B&B, in the meantime, discover a grated walkway that could have scraped the victim. They follow it to Nadia's cabin, where the cougar is busy getting busy with a man half her age. Booth shoos out the boy and then spots maggots in a nearby closet. Could Liam's body have been left to rot in the space? "I think he was killed and stashed in there until they got out deep enough to dump the body," Booth theorizes. Second later, Booth and Sweets grill Nadia in the interrogation room. "If something happened to Liam that night, I don't know what it is," Nadia says. She suggests they talk to Captain Kelly (Dave Florek), who is apparently the only person with a key to the maggot closet.
So Kelly is brought in for questioning, but denies any knowledge of Liam's death. It also turns out the maggots weren't feasting on human remains, but gourmet cheese from another party aboard the boat. Kelly does mention he spotted Liam on deck with a woman, but can't offer a decent description ... because he was drunk. Sweets' plan: get the captain drunk so he'll be in the proper state to remember (it's a shrink trick). So Kelly downs a bunch of booze and remembers the female had red hair. And who else has red hair? Claire Casper, wife of the man whose identity was stolen!
Before you can say "plot twist," Claire is in the hot seat. "I didn't kill Liam," she growls. "And there's nothing you can do to prove different." Hodgins then discovers the victim's bones are also streaked with some kind of glue: barnacle secretion. Hodgins and Daisy then act out their theory: Claire and Liam struggle ... Claire then stabs Liam with a boat hook ... Claire throws Liam overboard and he is scraped against the barnacles. A quick check of the barnacles reveals Claire Casper's blood!
The suburban housewife then admits to the crime. She killed the boy after he called her a "desperate old hag." Claire cries, but Booth remains stone faced. Case closed ... but not the episode. Sweets explains to Daisy that he can only continue to see her if they have "substantive conversation." The two then bond over their shared love of "Saved by the Bell" (seriously). It looks like the kids might just make it. Camille (Tamara Taylor), meanwhile, holds a press conference revealing that the slaves have all been identified. She reads off the names ... and stumbles over one who shared the same first name as her great-great grandmother. It's a very emotional ending.