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Marle is actually Princess Nadia, the daughter of King Guardia XXXIII, who rules Crono's home country. Frog is actually Glenn, squire to the lengendary knight Cyrus, who was killed in a battle with the wizard Magus; it was this same encounter that left Glenn in his cursed amphibian form.
Crono and company at first believe that Magus, who leads the monstrous Mystics in the year 600 A.D., was responsible for creating the all-consuming monster Lavos, but a series of mishaps proves them wrong. It seems as though Lavos fell from space and crashed into the Earth 65 million years B.C., then burrowed underground to wait until Earth's lifeforms had evolved to its liking.
An important subplot in the game involves the kingdom of Zeal, which thrived on a chain of skyborne islands 12,000 years B.C. Its people had harnessed the power of magic, thanks in part to Lavos. The widowed Queen Zeal sought to use her Mammon Machine to gain immortality from Lavos, but her daughter and son, Schala and Janus, knew that the creature was evil. In an attempt to thwart the queen's plans, Crono and friends confront the monster, and Crono is killed in battle. An arduous trip through various points in time allows our hero's comrades, with the help of the mystical Chrono Trigger, to revive their fallen friend. Once united, the group bands together with Magus (who, as it turns out, is actually young Prince Janus, thrown into the year 600 by Lavos) to destroy the so-called "infamous immortal" in a fantasic battle.
By the end of the story, we find out that Kino, Ayla's mate, and Doan, the caretaker of the Arris Dome in the year 2300 A.D., are both part of the royal Guardian bloodline. Also, the three Gurus of Zeal, Gaspar, Melchior, and Belthasar, are, respectively, the old caretaker of the End of Time, the weaponsmith of Crono's era, and the crazy inventor of the Epoch time machine. All three had been scattered throughout the timestream after an encounter with Lavos.