The story of Chrono Cross begins with Serge, who must collect komodo dragon scales on the beach for his friend Leena. The setting is El Nido, a tropical archipelago inhabited by ancient natives, mainland colonists, and beings called Demi-humans who are often prejudiced against. While meeting his friend, Serge slips into an alternate dimension in which he drowned on the beach ten years prior. While searching for truth behind his supposed death, Serge meets the famous thief, Kid, a teenage girl intent on finding the mysterious Frozen Flame. Serge joins her search.

The story of Chrono Cross focuses on a teenage boy named Serge and a theme of parallel worlds. Faced with an alternate reality in which he died as a child, Serge endeavors to discover the truth of the two worlds' divergence. The flashy thief Kid and forty-three other characters assist him in his travels around the tropical archipelago El Nido. Struggling to uncover his past and find the mysterious Frozen Flame, Serge is chiefly challenged by Lynx, a shadowy antagonist working to apprehend him.