When human remains are discovered in the belly of a shark, Brennan and Booth are brought in to identify the missing person. Evidence suggesting the victim had been the prey of several fish directs the team's investigation to The Aquarium of the Atlantic, where a guest lecturer and notorious self-help guru preaching the healing power of the ocean has gone missing. Meanwhile, both Brennan and Booth navigate their own relationship when a marine biologist shows interest in Booth.

After a skull and decomposing hands are found in a dumpster, the team must not only solve the crime but also search for the rest of the victim's remains. Identified as Ray Raminsky, the victim turns out to be a bounty hunter in search of Charles Braverman, a man indicted for the murder of a co-worker. Meanwhile, Brennan is asked by Professor Bunsen Jude "The Science Dude" if he can shoot an episode of his children's show from The Jeffersonian Lab with Brennan as his special guest. Brennan initially turns him down, but is surprised when he makes her a deal she can't refuse, so she takes him on as a new "squintern." As the team pieces together the details of the crime, they discover that they are not alone in the hunt for Braverman and find themselves in a chase with an unexpected suspect.

Metal hardware deliverer Tony Cole was fatally stabbed in a puzzling way. Booth is more preoccupied with his son Parker, finally back from England, and how to fit him in the family with Bones and baby sister Christine, and Sweets is through with counseling under false pretenses. Hodgins uses the case to prove his expensive 'pet' equipment is all useful. Tony had a bitter company rival, Karl Singler, and picked a fight with his beloved boy Danny's karate sensei, Hunter Sherman, over a fight with sprout Blake Sherman.