The plot of Adventures of the Deep revolves around a Pacific Legend known as the Song of Dragons. The player character, a university student studying folklore, takes leave from their studies to visit the Paoul Republic in the South Pacific, intrigued by the legend. By chance, they apply for a job at R&R Diving Service, run by Jean-Eric Rouvier and his granddaughter Océane. During the player's entrance examination dive, Océane drops a lapis lazuli pendant left to her by her late father Matthieu; the pendant omits a strange sound, after which a nearby humpback whale becomes aggressive. Curious, she disregards Jean-Eric's warnings and attempts to retrieve a second pendant lost as a child, only to be threatened by an aggressive tiger shark. The player is able to drive off the shark, and the pendant is recovered. Deciding to have the two pendants appraised, R&R contacts Nancy Young, a local trader, who suggests that they search for Valka Castle, which sank beneath the waves in the 17th century, for further clues.
Traveling to the Aegean Sea, the group encounters Gary 'GG' Gray, a famous American salvager, who challenges them to see who can find Valka Castle first. The player and Océane successfully discover the castle while trying to escape the man eating great white shark Thanatos, where they uncover an ancient lapis lazuli tablet and hear a strange sound before they are temporarily sealed in a room by a trap left by the castle's ruler. Encountering GG again following their escape, he reveals that the tablet originates from an ancient sea-faring civilization known as the Okeanides. R&R returns home, and Nancy recommends that the group consult Japanese oceanographer Hayoko Sakurai to have the tablet translated. Traveling to Hayoko's current workplace, an aquarium in Japan, she agrees to decipher the tablet in return for R&R completing her research on polar bears for her. After traveling to the northern coast of Canada and completing her research, Hayaoko joins R&R Diving Service and reveals her findings on the tablet; it tells that the Song of Dragons is the key to the Pacifia Treasure, a legendary treasure left by the Okeanides. Following reports of the song being heard in the Antarctic, the group travels there to investigate further. While investiagting, the player hears a strange sound they had previously heard while at Valka Castle, and realizes that it is the Song of Dragons. They help rescue a spectacled porpoise, which subsequently helps R&R navigate their way out of a heavy snowstorm. Upon returning home, Jean-Eric forbids any further investiation into the legend, declaring that it will only lead to bad luck. He privately confesses to the player that Matthieu had attempted to discover the Pacifia Treasure himself, which lead between him and Jean Eric, who dismissed the Treasure as a myth; Matthieu later died during his investigation when his submarine broke down.
The next morning, R&R receives an unexpeted visitor in the form of GG, who explains that he has been searching for the Pacifia Treasure for the past 10 years, and offers to work with R&R in locating it. Following a lead in South America, the player and GG swim upstream a tributary of the Amazon River, where they discover an ancient ruin behind a waterfall and uncover a second lapis lazuli tablet.