Plot
In 1000 AD, Crono and Marle watch Lucca and her father demonstrate her new teleporter at the Millennial Fair in the Kingdom of Guardia. When Marle volunteers to be teleported, her pendant interferes with the device and creates a time portal into which she is drawn. After Crono and Lucca separately recreate the portal and find themselves in 600 AD, they locate Marle, only to see her vanish before their eyes. Lucca realizes that this time period's kingdom has mistaken Marle (who is actually Princess Nadia of Guardia) for Queen Leene, an ancestor of hers who had been kidnapped, thus putting off the recovery effort for her ancestor and creating a grandfather paradox. Crono and Lucca, with the help of Frog, restore history to normal by rescuing Leene. After the three part ways with Frog and return to the present, Crono is framed for kidnapping Marle and sentenced to death by the current chancellor of Guardia. Lucca and Marle help Crono escape prison, haphazardly using another time portal to evade their pursuers. This portal lands them in 2300 AD, where they learn that an advanced civilization has been wiped out by a giant creature known as Lavos that appeared in 1999 AD, and find the last remnants of humanity living in underground domes subsisting off of machine energy in place of food. The three vow to find a way to prevent the future destruction of their world. After meeting and repairing Robo, Crono and his friends find Gaspar, an old sage residing in an atemporal space known as the End of Time, who offers them the ability to travel through time by way of several pillars of light. (The party is able to challenge Lavos at any point after this scene, with completion of the game prior to its final chapter unlocking one of twelve different endings.)
The party discover that a powerful mage named Magus summoned Lavos into the world in 600 AD. To stop Magus, Frog requires the legendary sword, Masamune, to open the way to the mage's castle. In search of ore to re-forge the sword, the party travel to prehistoric times and meet Ayla, the chief of an ancient hunter-gatherer tribe. The subsequent battle with Magus disrupts his spell to summon Lavos, opening a temporal distortion that throws Crono and his friends to prehistory. The party assist Ayla in battling the Reptites, enemies of prehistoric humans. The battle is cut short as the party witness the true origin of Lavos, who descends from deep space and crashes into the planet before burrowing to its core. Entering a time gate created by Lavos's impact, the party arrive in the ice age of 12,000 BC. There, the utopic Kingdom of Zeal resides on islands raised above the icy surface using energy harnessed from Lavos's body beneath the earth's crust via a machine housed on the ocean floor. The party are imprisoned by the Queen of Zeal on the orders of its mysterious Prophet, and are ultimately banished, with the time gate leading to 12,000 BC sealed by the Prophet. Seeking a way to return, the party discover a time machine in 2300 AD called the Wings of Time (or Epoch), which can access any time period at will. The party return to 12,000 BC, where Zeal inadvertently awakens Lavos, leading the Prophet to reveal himself as Magus, who tries and fails to kill the creature. Lavos defeats Magus and kills Crono, before the remaining party are transported to the safety of the surface by Schala, Zeal's princess. Lavos annihilates the Kingdom of Zeal, whose fallen continent causes devastating floods that submerge most of the world's landmass.
Magus confesses to the party that he used to be Prince Janus of Zeal, Schala's brother, and that in the original timeline, he and the Gurus of Zeal were scattered across time by Lavos's awakening in 12,000 BC. Stranded as a child in 600 AD, Janus took the title of Magus and gained a cult of followers while plotting to summon and kill Lavos in revenge for the death of his sister. Magus tried once more after the party's battle in his castle returned him to Zeal, where he disguised himself as the Prophet. At this point, Magus is either killed by the party, killed in a duel with Frog, or spared and convinced to join the party. The ruined Ocean Palace then rises into the air as the Black Omen, Queen Zeal's floating fortress. The group turns to Gaspar for help, and he gives them a "Chrono Trigger", a device that allows the group to replace Crono just before the moment of death with an identical doppelgänger (doing so is optional, and the game's ending will change depending on the player's decision). The party then gather power by helping people across time with Gaspar's instructions. Their journeys involve defeating the remnants of the Mystics, stopping Robo's maniacal AI creator, giving Frog closure for Cyrus's death, locating and charging up the mythical Sun Stone, retrieving the legendary Rainbow Shell, unmasking Guardia's Chancellor as a saboteur, restoring a forest destroyed by a desert monster, and preventing an accident that disabled Lucca's mother. The party then enter the Black Omen and defeat Queen Zeal, after which they battle Lavos. They discover that Lavos is self-directing his evolution via absorbing DNA and energy from every living creature before razing the planet's surface in 1999 AD, so that it could spawn a new generation to destroy other worlds and continue the evolutionary cycle. The party slay Lavos, and celebrate at the final night of the Millennial Fair before returning to their own times.
If Magus joined the party, he departs to search for Schala. If Crono was resurrected before defeating Lavos, his sentence for kidnapping Marle is revoked by her father, King Guardia XXXIII, thanks to testimonies from Marle's ancestors and descendants, whom Crono had helped during his journey. Crono's mother accidentally enters the time gate at the Millennial Fair before it closes, prompting Crono, Marle, and Lucca to set out in the Epoch to find her while fireworks light up the night sky. If Crono was not resurrected, Frog, Robo, and Ayla (along with Magus if he was recruited) chase Gaspar to the Millennial Fair and back again, revealing that Gaspar knows how to resurrect Crono; Marle and Lucca then use the Epoch to travel through time to accomplish this. Alternatively, if the party used the Epoch to break Lavos's outer shell, Marle will help her father hang Nadia's bell at the festival and accidentally get carried away by several balloons. If resurrected, Crono jumps on to help her, but cannot bring them down to earth. Hanging on in each other's arms, the pair travel through the cloudy, moonlit sky.
Chrono Trigger DS added two new scenarios to the game. In the first, Crono and his friends can help a "lost sanctum" of Reptites, who reward powerful items and armor. The second scenario adds ties to Trigger's sequel, Chrono Cross. In a New Game Plus, the group can explore several temporal distortions to combat shadow versions of Crono, Marle, and Lucca, and to fight Dalton, who promises in defeat to raise an army in the town of Porre to destroy the Kingdom of Guardia. The group can then fight the Dream Devourer, a prototypical form of the Time Devourer—a fusion of Schala and Lavos seen in Chrono Cross. A version of Magus pleads with Schala to resist; though she recognizes him as her brother, she refuses to be helped and sends him away. Schala subsequently erases his memories and Magus awakens in a forest, determined to find what he had lost.