Set in the southern coast of California at the Harding Pencroft Academy, the novel follows a young student called Ana Dakkar. Ana and her brother lost their parents two years ago in a tragic sea exploration accident and to wish her good luck for her first true practical introduction to the life of the sea, her brother, Dev, gifts her their mother’s necklace.
A class of freshmen students get aboard to explore the depths of the ocean as their academy suddenly falls under attack and gets destroyed. Among the survivors are Ana, a prefect Gem, her best friends Ester and Nelinha, professor Dr. Hewett and a dozen other students. They soon realize that the attacker was the rival academy, the Land Institute, and that they are in danger as well. They get aboard a submarine and quickly escape into the open sea.
As they are escaping their enemy, Dr. Hewett explains that this sort of attack was expected since two years ago. He also reveals that Captain Nemo from Jules Verne’s novels was a real person and that the main motive is the knowledge and heritage he left behind, that is in direct possession of Harding Pencroft, including the Nautilus submarine. But the most striking is the fact that Ana Dakkar is the direct descendant of Captain Nemo and key to unlocking the knowledge he left behind.
Out in the ocean, the remaining survivors suffer another attack by the enemy, Dr. Hewett falls into a coma and Ana is put in charge to help get them to safety. Safety lies on the hidden island, included in one of Verne’s works, where the Nautilus and the remainder of Nemo’s heritage lies. Slowly but surely, they reach the hidden island, which is occupied by Ophelia and Luca, Ana’s parents’ friends who witnessed their death. Ana’s parents died trying to enter the Nautilus submarine, which was hidden close to the island, abandoned at the bottom of the ocean. The crew learn that Nautilus is a conscious being, an AI, and Ana is the only one who can control it/her. The reparation of Nautilus start while Ana is coping with the truth about her parents.
Suddenly, the island gets also attacked by the enemy, and the captain of the opposing submarine is none other than Dev, Ana’s brother whom she thought dead when the Harding Pencroft Academy fell. It turns out that he was the main person behind the attack, and the reason why he was able to follow Ana and the crew is the necklace around Ana’s neck, which he gave to her right before the attack. Ana and a few others of the crew get aboard Nautilus and encourage her to start and get them out of there into the open ocean. They manage to escape with Nautilus special technology which enables them to travel long distances very quickly.
The Nautilus stops somewhere near the Philippines. While there, Ana and the rest devise a plan to return to the island to rescue the rest of the crew and defeat the enemy. They get unlikely support from a giant squid, brought upon by Nautilus. Ana calls the giant squid Romeo, and they decide to use his help as a secret weapon against the enemy.
They return to the island, a battle ensues and Dev and the Land Institute students are defeated. Ana and Ester decide to rebuild Harding Pencroft Academy and train in preparation for another inevitable enemy attack. Ana takes Dev aboard the Nautilus, where they have a conversation about their family and inheritance, but their trust is forever broken.
