The following version of the book was used to create this study guide: Riordan, Rick. Daughter of the Deep. Buena Vista Books, New York, NY, 2021. Kindle AZW file.

Ana Dakkar is a freshman at Harding-Pencroft Academy, an elite school that grooms students for jobs in marine-related fields. Her older brother Dev is also a student there. Ana and Dev are close because their parents died a couple of years earlier. One morning, Dev gives Ana a gift – a necklace made from their mother's pearl. He says it is to wish her luck for the upcoming freshman trials. This is a series of of tests freshmen have to pass in order to continue studying at HP. When Ana and her fellow freshmen are on the way to the dock where the HP ship Varuna is kept, she looks back toward the campus just in time to see missiles traveling through the water and the campus property collapse into the ocean. Their bus pulls over. Their teacher, Dr. Hewett, says he had been afraid of an attack of this time. He reveals that Land Institute (LI), HP's rival, is behind the attack. He surprises everyone when he arms all the students who specialize in warfare and orders them to protect Ana at all costs. Ana and the others are in shock, partly because of the destruction but also because some of them had siblings on campus who are probably now dead.

Ana and the others set out aboard the Varuna, and Hewett begins to make revelations. Jules Verne's story of Captain Nemo was real though there were a few inaccuracies. The Nautilus and all of Nemo's technology exist. HP and LI have been in a race to recreate and control the technology. Ana is Nemo's direct descendant, meaning she can operate some of the DNA-specific technology. Hewett makes it clear Ana will be making the decisions. However, before he can offer further guidance, he falls ill and winds up in a coma. Ana, with support from her best friends Ester and Nelinha, agrees to use the technology to find Nemo's secret island which HP controls, now known as Lincoln Base. The students arrive to find that the Nautilus is actually a living submarine and that two HP staff members have been restoring the sub for the past couple of years. Before Ana and the others can participate in a test run, LI students arrive. Ana discovers that Dev is a traitor working with LI. Over the coming days, Ana and her team manage to leave Lincoln Base in order to keep the Nautilus out of the hands of LI. While there are some discussions about whether it is right to hide this technology from the world, Ana realizes that the world is not ready to use it responsibly.

Ana and her crew regroup and make plans before returning to Lincoln Base. They have help from a giant octopus, a dolphin, and some “bug” drones that ensure the HP students are victorious. As the novel comes to an end, Ana and Ester announce they plan to rebuild HP but with some changes to the school's policies. All her classmates agree to remain as part of the team. Ana releases all the LI students but keeps Dev nearby, knowing she cannot trust him on his own. She takes Dev aboard the Nautilus, showing him what he has thrown away by joining LI.