Story. MASS FUCKING SPOILERS, I'M NOT BOTHERING WITH A TAG.
You go back in time to save a cute girl, and then keep her from being time-paradoxed. You meet a strange frog-knight, who helps you to rescue the queen, and who then leaves in shame. Then, after bringing her back to the future, the king goes nuts, as this cute girl is actually HIS DAUGHTER, and you're forced to flee, after being framed by the advisor, leaping into a time portal.
You find yourself in a POST APOCALYPTIC FUTURE.
You fight through these bizarre, but terrifyingly, depressingly familiar cities, and discover that a single creature did this, a creature known only as Lavos.
You manage to make your way back to the past- and discover yourself at the End of Time, meeting an old man standing alone in a dark street corner, surrounded by black infinity.
Then you recover an ancient lost power, forgotten to mankind for thousands of years... Magic. Fortified this way, you return to the present, and fighting your way back home through the lost remnants of an ancient army of monsters, you discover that a mysterious man named Magus, a deadly powerful warlock known only in stories, was the one who summoned Lavos.
You fight your way through time and space, meeting the odd man-frog from before who helped you to indirectly save Marle before, and help him to regain an ancient sword of epic power, the Masamune, defeating it's twin guardians, and retrieving a weapon written of in legends. You travel into the past to find the rare mineral needed to repair it, and meet a clan of humans from the earliest histories, and help them to fight an utterly evil saurian named Azala. You manage to beat him, and travel back to the present, repairing the sword. You return it to Frog, and learn of his tragic past, becoming a knight of the kingdom, but watching his best friend, Cyrus, be murdered by Magus in front of his eyes, and being turned into the creature he is now. Frog uses it to cut a mountain in half, and you venture in, to face an evil beyond words.
You fight your way through a castle, eventually coming face to face with Magus as he casts his spell, and ending up beating him, breaking his concentration.
And you learn that Magus didn't create the creature, he was only awakening it. The beast, Lavos, has been living on our planet for millions of years.
You awaken in the past, with your friend Ayla, and learn that the Reptites are on the offensive. You join her in a last ditch attack against the Reptites, to free her clansmen and her lover, Kino. As you fly off to face them, an eery red star glows in the sky...
You fight valiantly, and eventually, you manage to defeat Azala. In the end, he refuses help, dying as the red star falls, cursing humanity to the end. And Ayla reveals- The red star is Lavos, a creature of unbelievable power, from a distant star, come to drain the world of it's life. You run to the impact crater, but Lavos has already burrowed deep, leaving only a solitary gate. You enter it, travelling through... and find yourself in a frozen wasteland, thirteen thousand years ago, massive continents in the sky blotting out the sun.
End of Act One.
You travel through the land, and discover massive gates to the continents above, and learn of the ancient civilization of Zeal- no longer a myth, but reality. What's more, you learn that they're harnessing the power of Lavos for their own purposes, and that he is the power behind the magic. You eventually meet a strange young man, who foresees the death of one of your party soon, and travel to the capital city, after seeing the Blackbird, a gigantic airship, a terror beyond terrors.
You find that the pendant that started all this, the royal pendant of Guardia, has the same properties as the pendant Schala, a beautiful yet tragic princess has, absorbing the energies from the Mammon Machine, a strange machine which harnesses the powers of Lavos itself, and you enter the throne room. The mysterious, yet somehow familiar prophet tells the queen that you are the ones he warned her about, and tells her to kill you- Dalton, her right hand man, summons a golem, a bizarre interdimensional creature, and when that fails, he traps you in a warp. You're left floating above the Mammon Machine, until the Prophet forces Schala to remove the three of you, take you back to the portal, and forces her to shut it after you.
You make a furious search through time and space, eventually finding the Epoch, and the last of the three Wise Men, in the future. Balthasar has already died, transferring his conciousness to one of the Nus- bizarre creatures you've seen throughout your travels. He helps you to open the Epoch, and aids you in starting it up. Now, with a way back to 12000 BC, you travel there. You travel to the Earthbound Ones home, and go on to save the wise man, Melchior, apparently an iteration of him from before your previous meeting. You climb the Floating Mountain, and manage to defeat the monster guarding him, after fighting your way through it's bizarre landscape- and sending the mountain crashing down, causing a massive tsunami. You watch Schala be kidnapped in front of your eyes, by Dalton- and are given a red knife by Melchior. You race to Zeal, to stop the Ocean Palace from being activated- as close to Lavos as it is, the Mammon Machine will almost certainly awaken him.
You fight Dalton, making your way into the ocean palace, fighting through countless dangers, as the queen prepares the Mammon Machine... and you see the three wise men gathered once more in the ocean palace. You fight to the end, and at the last moment, manage to strike the red knife into the Mammon Machine. The coursing energies surge through it, and it transforms- into the Masamune that Frog still carries.
But it's not enough. Lavos rises, and Zeal commands him, completely insane at this point. Your party fights, hard, valiantly, but it's all for nothing- the insane god-beast devestates you without even trying. The Prophet reappears, and reveals himself... as Magus. Hungry for revenge, and willing to face death to do it, he uses an ultimate strike on Lavos- for nothing. You, your friends, Magus, and Schala lie, nearly dead, as Zeal laughs in triumph.
And then Crono stands up. Body on the verge of failing, barely able to walk, let alone fight, he challenges Lavos, and before everyone's eyes, dies- obliterated in a flash of light. And Schala, desperate to save you, uses the last of her energy to save the party and Magus, and then disappears.
And Lavos awakens. He rises from the sea, and destroys the floating continent of Zeal, annihilating it effortlessly, reducing the greatest civilization the world has ever known to rubble within minutes. People fall, and the continent falls with them, collapsing into the sea.
End of Act Two.
The party awakes... and Chrono is gone. Still gone. Marle nearly loses it, the whole party mourning the loss of the one odd young man who united five people from across space and time to face a god, and paid the ultimate price. They band together, and go to meet the elder of the Last Village. Suddenly, at the worst possible time, Dalton appears, claims the Epoch, and sucker-punches your party. You wake, weaponless, forced to sneak through the Blackbird, in flight, getting your equipment back. You face off against Dalton, destroying him in a rage, and finding that the Epoch has been altered so it can fly.
You travel back to the Last Village, and as you land, you see a strange disturbance in the water...
A massive black ship rises into the upper atmosphere. The Black Omen. The physical representation of evil, of the Ocean Palace, of Zeal... of Lavos. You meet Magus, and bury the hatchet, and learn of one chance that you have in the End of Time- The Chrono Trigger. You go to the present, and borrow Chrono's clone. You travel to the future, and meet Balthasar in the Nu's body. He helps you one final time, and then has you shut down the Nu, finally giving it an eternal rest.
You climb Death Peak, helped by the last program of the Nu, and discover what Lavos gathered its energy for.
You fight the spawn, killing each of the three, and reach the peak. Then, as you prepare the ritual... The Chrono Trigger, the fragile egg on which all of your hopes and dreams stand, shatters.
And as they stand there, everything seeming hopeless, the sun is slowly eclipsed.
And they find themselves, back at that fateful moment, just before Crono died- and they pull him out of the time stream, replacing him with the clone. Crono and Marle embrace, Crono back from the dead, Marle having saved him like he saved her, a lifetime ago. And as they walk down Death Mountain, they prepare for the most difficult battle of their lives- the battle against this creature, this thing, that's been living off of their planet for time immemorial.
In 600 AD, they help a woman turn a desert into a paradise, Robo spending four hundred years to replant the forest, and Lucca saving her mother- and a hint, just a possibility, that the gates are not the effect of Lavos, but the memories of the planet itself, having it's life flash before it's eyes...
In 65 million BC, you start a chain of events, charging an ancient stone with sunlight, creating one of the most incredible sources of magical power in the world.
Cyrus' ghost is helped to be put to rest, by rebuilding the ancient castle where it resides, finding ancient, powerful weapons, and helping to unlock the true power of the Masamune, making it a weapon to be reckoned with.
Ozzy, Flea, and Slash, are finally put to rest in 600 AD.
Robo confronts his demons, finding his birthplace, and destroying his old companion and his creator, stopping a diabolic plot by the robots to destroy what remains of humanity in 2300 AD.
In 600 AD, you help an explorer find the mythical Rainbow Shell, and in 1000, you call up his ghost to retrieve the rainbow shell, fighting the ancient remnants of the Reptite civilization. Then, you help save Marle's father, King Guardia, from the machinations of the advisor- the evil Yakra 13, thirteenth iteration of the Yakra you defeated, so very long ago, taking the form of the king's advisor just like the first. After a ferocious battle, the rainbow shell is revealed, safe and sound, and a set of truly awesome weapons and armor are made, including the Rainbow Sword- a weapon that, in it's time, would become a legend itself.
Finally, flying to the Black Omen, a constant throughout time and space, you fight your way through the twisted, non-euclidean vessel, confronting Queen Zeal, the Mammon Machine, and then Zeal's true form, in a final, apocalyptic battle, on the deck of the Black Omen, hovering above the atmosphere.
And finally, you face Lavos. The creature that has constantly stayed one step ahead of you, the creature that has devestate humanity three times. And as you shatter it's shell, you discover the truth- The creature has been manipulating humanity for millions of years. Every action, every moment of your lives, orchestrated by this creature for it's own feeding. In a violent rage, you fight the creature, and manage to defeat it.
But Lavos has one last trick up it's sleeve. It calls you into a time warp, rushing past all the significant moments in time that you've seen it's influence, and you fight it, in the most earthshattering battle the world has seen.
Finally, you manage to beat it, defeating the creature that would destroy the world, and simultaneously save the present, past, and future- changing the grim apocalyptic world into a new one. The group says their goodbyes, and they get into the epoch, to search for the final necessary link, getting Crono's mom back after the stupid bitch jumped through the fucking portal, after the dumbass cats.
Lucca, Marle, and Crono go on to live lives, and are remembered as the three kids who saved a world.
Frog searches for a cure to his form, without having to kill Magus.
Robo and Atropos are happy in the future, living in a beautiful world of peace, a utopia.
Janus, Magus, continues searching for his sister, hoping to find Schala at last.
Ayla goes back to her time, raising a strong family, a dynasty that will last far into the future.
And a child cries in the woods, as Lucca comes upon a young baby girl, with strange blue hair.