Chrono Trigger's seven playable characters come from different eras in the game world's history. Chrono Trigger begins in 1000 A.D. with Crono, Marle, and Lucca. Crono is the silent protagonist, characterized as a fearless young man who wields a katana in battle. Marle lives in Guardia Castle; though sheltered, at heart she's a princess who enjoys hiding her royal identity. Lucca is a friend of Crono's and a mechanical genius; her home is filled with laboratory equipment and machinery. From the era of A.D. 2300 comes Robo, or Prometheus, a robot with near-human personality created to assist humans. Laying dormant in the future, Robo is found and repaired by Lucca. He joins the group out of gratitude. The fiercely confident Ayla dwells in 65,000,000 B.C. Unmatched in raw strength, Ayla is the chief of Ioka Village, and leads her people in war against a species of humanoid reptiles known as Reptites.

The last two characters are Frog and Magus. Frog originated in A.D. 600. Frog is a former squire once named Glenn; Magus turned Glenn into an anthropomorphic frog and also slew his friend Cyrus. Chivalrous but mired in regret, Frog dedicates his life to protecting Leene, the queen of Guardia, and avenging Cyrus. Meanwhile, Guardia in A.D. 600 is in a state of conflict against the Mystics (known as Fiends in the US/DS port), a race of demons and intelligent animals. Under the leadership of Magus, a powerful sorcerer, they wage war against humanity. While Magus appears to be a powerful magician, his seclusion conceals a long-lost past; in the Dark Ages, he was known as Janus, the young prince of the Kingdom of Zeal, which was destroyed by Lavos in 12,000 B.C. The incident sent him forward through time, and as he ages, he plots revenge against Lavos and broods over the fate of his sister, Schala. Lavos, who awakens and ravages the world in A.D. 1999, is an extraterrestrial parasitic creature that harvests DNA and the Earth's energy for its own growth.