Return to Mysterious Island 2 begins with the crash of the helicopter that came to rescue Mina. She survived but is once again trapped on the island. All of a sudden, under her very eyes, an unknown disease afflicts the plants first, then the animal life. Mina explores the island to locate the infection source. She searches Captain Nemo's base in vain, then the ruins of an unknown civilization, and finally understands that it is outside pollution that threatens the island. The only way to save this natural wonder is to turn the shield back on. But if Mina makes this decision, she gives up -as Captain Nemo did before her- the idea of returning to civilization…

Two-character play: in the first installment, the player embodied Mina, a young and carefree navigator taking part in the Jules Verne competition, and used Jep, a cute, little monkey, as a simple tool. In Return to Mysterious Island 2 Jep becomes a character in his own right. The player switches from one character to another and maximizes the use of each other’s talents depending on the circumstances: only Mina can use complex tools, combine objects and, of course, read the documents found in the course of the game; whereas Jep can climb places inaccessible to Mina, communicate with other monkeys and find numerous objects thanks to his sense of smell.