Agent Seeley was snug in bed sleeping when he was awakened by a beating on his apartment door by an excited Agent Bones who wanted to fill him in on the latest case assigned to the Jeffersonian. Seeley crawled out of bed wearily and dressed in his bedroom while Bones told him that a sunken ship, the Amalia Rose, had been discovered and a large group of old bones had been brought in to the lab. The forensics experts were to identify the bones belonging to a long dead shipment of slaves from the eighteenth century.
Once at the lab, the agents began the arduous task of separating the tangled bones into individual skeletons which would take quite a lot of work. Gradually, each agent was able to accomplish that task, Bones finding a skull covered in pink sea life, supposedly some kind of small worm. Agent Hodgins was ecstatic, thinking that he may have come across some kind of alien life form, which the other agents immediately pooh poohed, making light fun of his supposition, but he stuck to his theory, and began immediately to try to identify it. He finally figured out it was something called oceanic pink snotflower which did not endear it to the other agents. The worm would settle on bones it located in the sea, attach itself to the bone and begin to suck out the marrow, which is what it apparently lived on. It had done so to this skeleton's marrow and Bones announced that this particular skeleton was less than a month old. She said that this was a murder and needed to be investigated immediately.
Bones discovered, upon closer examination of this skull and bones, that many old fractures had been incurred on it which apparently had not healed adequately, indicating past child abuse, and that this had been a young man, no older than nineteen or twenty years of age, which made her suspicious. A match was made of missing adult males, and supposedly one Mike Casper was identified, but he was twenty eight years old, but nevertheless, he and his wife were interrogated at their home. Casper had filed charges of someone using his identity and stolen his credit cards, so he was in the system, but he was not missing. He vehemently denied knowing any young man of such identity, but was brought in for further questioning. He was released as was his wife, because nothing conclusive was found during their interrogation. That left the agents going back to the skeleton. Once again, Agent Bones looked at the old fractures, coming up with the bright idea of using missing children's files to identify the bones. That computer search brought up one missing foster child, Liam Maloney, who had been found not long after that missing report had been filed. That child's face was positively Maloney, but who had murdered him and why?
Bones also found out that the victim, upon closer examination of the skull, had been hooked through the mouth by something sharp that had gone up into his brain, thereby killing him. The bones bore sharp deep scrapes, reminiscent of a large grater, which left the agents very puzzled. Those later proved to be barnacles that had stuck themselves to the bones.
Bones and Seeley walked into Sweets' office without knocking, only to find a very naked pair of Sweets with Daisy on top of him, having sex. The two clothed agents were a bit shocked and Bones told the two to get dressed and meet them out in the common area. Two shamefaced young people met the older agent's glances with hooded eyes as the case was explained further to them, prompting Sweets to stutter out a rapid fire explanation of the previous situation where upon Seeley told him to shut up, that they didn't care about that. Sweets did just that as Bones told him that he, Seeley and Bones were going to go question one Hunter Lange, bar tender on a cougar cruise ship, about what he might know of the murder of Maloney.
The three agents, that afternoon, approached the cruise ship and chatted with Captain Kelley, captain of the ship, about Lange, and asked permission to climb aboard and question the young man. Captain Kelley nodded his assent and the agents mingled with the middle aged women and twenty something men on board, finding Lange behind the ship's bar. Seeley found out from Lange that the young man had not seen Maloney for about a month and didn't have a clue as to his whereabouts. Leaving the bar, Seeley mingled with the passengers, finding Bones drinking a pink martini and chatting with an amorous young man who seemed very interested in her. Trying to discourage the youngster, Seeley watched a very enthusiastic Bones walk off with him, leaving Seeley to fend off a middle aged woman passenger himself. Once free of her, he snagged Sweets from another would-be amorous woman and going downstairs to locate the female cruise ship owner, Nadia, and hearing some moaning coming from a nearby stateroom, they broke into the room and found Nadia on the bed with a young man on top of her. Telling the two on the bed to get dressed, Seeley was distracted when the other agent found some maggots on the carpeted floor by the closet, supposing they were corpse maggots. Interrogating the captain a bit later, he began to laugh and told the agents that once a month, he captained a gourmet cruise and had had some illegal Italian cheese hidden in that particular closet. Agent Bones said she knew of this cheese bearing live insect larvae and that the maggots found had proven to be just that, not corpse maggots. When asked when he had last seen the victim, Captain Kelley said that he had been quite drunk and had seen the young man with a middle aged woman with red hair. Agent Sweets told Bones and Seeley that if the captain were given enough alcohol to get him as drunk as he had been that night, that he just might remember more details. The agents agreed to do that and when drunk enough, the captain said that Maloney had been with Claire Casper, Mike's wife. She was brought in for questioning.
Hodgins came upon the bright idea of using piranhas to chew the pink snotflowers off the victim's bones, which seemed to work very well. He was ecstatic about coming up with the idea.
Claire Casper admitted to having an affair with Liam Maloney. She said that the young man would come by nearly daily after he knew her husband, Mike, had left for work. She claimed that Maloney had told her he had a thing for older, mature women and wanted to get to know her better. She found out he was a regular on the cougar cruise ship and went to scope the scene out. She joined the cruise and continued her affair with Maloney on the ship. One time out at sea, he argued with her and they fought. The fight continued out on the deck of the ship, Maloney somehow finding himself in the water. Claire told the agents later, she had wanted Maloney dead but did not want to kill him herself. She confessed to grabbing a boat hook nearby and using it to try to help Maloney aboard, but instead accidentally hooking him in the mouth with the boat hook, thereby killing him. She did not know what to do at that point, just letting the body sink into the water and not calling out for help. Claire broke down, crying, as the agents looked at one another.
Hodgins, meanwhile, used bone marrow extracted from the barnacles scraped off the victim's bones to identify as coming from the victim, and together with Claire's confession of murder, it was enough to convict her.
Angela Hodgins had been making sketches of each of the slaves as they were identified and at the presentation for such at the end of the show, each sketch was shown and some knowledge of them, plus their names, were given to much applause from attending family members and patrons.
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