1000 A.D.
Crono awakens to his mother calling him, and she reminds him of the Millennial Fair, and that his friend Lucca asked to speak with him when he woke up.  She gives him some money and he leaves.  He then travels to Lucca's house, and finds her there.  Lucca presents to him her prize invention, the Super Dimension Warp, which she will be demonstrating at the fair that afternoon.  Lara, Lucca's mother, calls from the back room, and Crono leaves.  Crono spends a few moments outside, and then goes to the fair. Crono arrives at the fairgrounds, and sees a man selling weapons named Melchior.  Crono examines the weapons, and Melchior replaces Crono's badly-made blade with a new one, the Rainbow Blade.  Crono thanks him and goes to the next section of the fair, where he bumps into a girl named Marle, on the run from guards.  He returns her dropped pendant to her, and she asks him to help her.  He does, guiding her further in to Lucca's demonstration.  Just as Lucca begins her presentation, Crono and Marle are about to leave; however, Lucca calls Crono to be her first volunteer, and Crono goes onstage to be a test subject.  He makes it through fine, but several guards spot Marle on the podium and she backs into the transporter pod, hoping to use it as a distractionary escape device.  However, when Crono hits the power, the electricity reacts with her pendant, causing a timewarp to suck her in.  Crono goes in after her, while a guard trips the power wires and causes the warp to close.  The guards clear the platform.

2300 A.D.
Crono arrives in the destroyed world and looks outside to see the decimation.  After a short scene back in 1000 A.D. with Lucca and the King, Crono hears a scream from the area below, and he runs downstairs to find Marle being attacked by two machines.  He quickly dispatches them, and helps her bind her wound.  Two more machines catch them off-guard, but Lucca destroys them with her powerful gun.  Crono stays with Marle until she can move, while Lucca decides to take a look around and see what she can find.  She enters the control room of the dome and finds a peculiar device from the future, a portable artificial being she names Robo.  She then is shown a video of Lavos destroying the world in 1999 A.D.  She gets Crono and Marle to look at the video, and they all decide they have to defeat Lavos before he can do anything.  They decide to go back in time as far as possible, so Lucca turns the power onto max on her Gate Key for maximum traveling capacity, and they all step through, Crono carrying the injured Marle.

600 A.D.
They arrive in the Middle Ages, and look out at the hills and trees, recognizing certain geographical features from their own world.  They descend the mountain and Robo says it's 600 A.D., recognizing that the castle is still under construction.  They continue to the base, and Marle finally begins to walk on her own, as they head for Guardia castle to seek assistance.  At the castle, the Chancellor mistakes Marle for Queen Leene and starts to have Lucca and Crono arrested, but Leene comes and sees how similar they are, as well as Marle's pendant, which is the same as hers.  In the throne room, Lucca reveals to the King and Queen that Marle is actually 1000 A.D.'s Princess Nadia, Leene's great great great great great great great great granddaughter.  Lucca then mentions their hunt of Lavos, and the King and Queen mention the war with the Mystics and their leader, Magus, who is attempting to summon Lavos to do his bidding.  The King says that only the Hero wearing the seal of Guardia and wielding the sword of magic can destroy Magus, and that they have yet to find him.  Just then, the Guardia captain arrives, saying that Mystics are about to enter the bridge.  The King orders all remaining troops to the bridge, and Crono and Lucca offer to fight.  Marle wants to as well, but Queen Leene has her taken to the infirmary, and Crono and Lucca rush off to battle.  
At the bridge, the skeletal monsters break through the last barriers, and Lucca uses her gun to decimate their ranks, blowing holes in the infantry.  The remaining warriors are picked off by Crono and the other soldiers, who eventually win the battle.  However, the bones gather together into a larger enemy, the Zombor, and the soldiers all flee in terror.  Crono and Lucca attempt to fight it, Crono even striking a good blow, but they are overwhelmed.  Suddenly, a strange warrior comes in and kills it with a single slash, the power of magic visible in his attack.  They approach him, and he is revealed to be the half-frog, half-man Hero, though he does not give them his name.  He says he will help them defeat Magus, but that he needs the Masamune, and that it is in the sacred site of the Denadoro Mountains, a place he cannot enter as a result of the curse upon him.  They offer to help him, and he awaits them on the bridge (after telling them his name), as they continue towards the Mountains.
At the base of the sheer cliff, Marle, still partially injured, joins the two again, wishing to come with them.  They ascend the steep rock, almost tumbling downward several hundred feet, but make it safely to the top, which leads into a cave lined with magic torches.  Lucca is unharmed by the fire, but Crono is not, and they go further in to find the Masamune.  Crono attempts to take it, but his other hand gets burned from the powerful light shining down on it, and the two spirits inherent to the blade, Masa and Mune, come out to test the three.  They attack them one by one with magic, thus releasing their inherent magical abilities of Water, Fire, and Lightning.  Afterwards, having proven themselves, the characters receive the Masamune, and are lifted out of the cave, floating gently to where Frog is standing on the bridge.  They give him the Masamune and he receives the magical powers of the blade, the element of Wind.  They then rest for the night, and Frog has a dream about his transformation and the death of Cyrus.  The next morning at Magic Cave, Frog uses his weapon to split the mountain, and the four move through the tunnel under the water towards Magus' castle, reaching the tower and entering.  Inside, Magus' voice beckons them forth, and at the top of the steps, the four use a magic transporter to enter his summoning chambers.  Magus chants while they walk forth, blue flames lighting up as they walk towards him, and finally all five are revealed.  Frog and Magus have some words, and then they fight for several minutes, until Frog finally slashes Magus across the chest, weakening him.  Just as Frog is prepared to deliver the final blow, Lavos wakes up and sucks the five into a massive timewarp, Magus revealing that Lavos is both ancient and not of his making.

End of Time
Crono and the others end up at the End of Time, the home of Gaspar, the Guru of Time, and a crossroads of time transport.  He tells them about the Conservation of Time, the Three Gurus of Zeal, Zeal itself, Lavos' curse upon that time, and Lavos' origin.  Marle, Crono, and Frog decide to go on to Zeal; Lucca stays behind to examine the area and do some other things, since only three may go at once.

12,000 B.C.
The three walk out of their enclosure into an icy, windy, dreary world.  Frog creates a tunnel of wind for them to pass through towards a structure in the distance, and they use it to find the structure is actually a portal into the sky, a skyway.  They transport from there to Zeal Palace, as Crono looks around for somebody in charge to speak with.  Marle does it the direct way and asks a stranger about Lavos, but he instantly goes into a rant about the horrible things the Queen would do if she heard such talk.  Schala comes and asks the three to follow her, and they enter her room.  She sees they are blessed with magic, and tells them about the Queen's plans to move the Machine into the Ocean Palace and how the Gurus said it was a bad idea.  After a short discussion, she decides to help them.  She leads them into a hallway where they can eavesdrop on the Queen's conversation, and they see a new person, the Prophet, come in, Zeal's new advisor.  The Queen asks Janus to fetch Schala, and Schala must go in order to give the appearance of order.  She then enters the room with her little brother, and the Prophet praises her ability to be the gateway for Lavos' power.  The three hear this and decide to leave for fear she's on the Queen's side, but Schala accidentally gives the three away.  The Prophet pulls them into the room with his powers and Schala pleads for their lives, saying she can send them back through the Gate.  Schala leads the Prophet and the three to the Gate, and the Prophet tosses them in, Schala being forced to seal the Gate once they're through.  She does, and expresses hope that they can return somehow.

End of Time
They end up at the End of Time, and ask Gaspar about a way to get back to the Dark Ages.  He says his friend Balthasar, the Guru of Reason, was building a device capable of transport through time, and it followed him through Lavos' timewarp into 2300 A.D.  Lucca gives Marle a crossbow and Frog decides to stay behind, having no desire to see the ruined world.  Marle, Crono, and Lucca enter the pillar.

2300 A.D.
The three end up in the Keeper's Dome, and find Balthasar's mechanical clone, the Nu, there.  The machine notices the Pendant of Zeal on Marle's neck, which he reveals has the power to control time, and the Nu then shows them the Epoch, Balthasar's last creation, telling them that he contains Balthasar's mental imprint and memories.  Before they go, he asks them to shut him down as his master's final wish, and Lucca does so, as the Epoch gets underway.  Lucca takes the controls and rockets them off towards the End of Time to pick up Frog.

End of Time
The three pick up Frog, say their goodbyes to Gaspar, and then go into the past.

12,000 B.C.
Lucca guides the group up into the clouds and towards Zeal Palace, dropping them off there and deciding to take the Epoch for a test spin while awaiting the others' return.  The three enter Zeal Palace, but find it entirely deserted, moving towards the huge black door at the end of the room.  It won't open (even by force), but Crono remembers the Nu calling Marle's jewel the Pendant of Zeal, and he uses it to make the door operate.  Meanwhile, Lucca and Robo (in the Epoch) engage an onslaught of aerial enemies, diving into the ocean to avoid destruction and witnessing the Ocean Palace from beneath the water.  Inside is Melchior, standing next to the transporter for the Ocean Palace, and Crono tells the others not to shoot.  Melchior explains that everybody has left, fearing the worst, while there is now no hope to end the threat of Lavos.  After some pushing, Melchior reveals that one weapon can defeat the Mammon Machine, the Rainbow Blade, but that he lost it some time ago.  Crono realizes that's his sword, and thanks the old man, as the three go to the Ocean Palace through the transport.  Melchior sees that perhaps his weapons of destruction can finally be used for good.
At the Ocean Palace, Crono and the others have to fight a hallway full of guards, decimating them.  From inside the Mammon Room, the Prophet realizes they have come, and as Crono, Marle, and Frog break through, a fight between Zeal's forces and themselves breaks out.  Crono ends up impaling the Mammon Machine and transporting everybody in the room to Lavos, who is now controlled, because of Crono's tampering, by Queen Zeal alone.  She attacks the group, but the attack is deflected by the Prophet, who reveals himself to be Magus, seeking revenge on Lavos for his evil.  He is unable to defeat the beast, however, and Schala risks her life to save the others.  Crono ends up sacrificing himself to freeze that moment in time, allowing the others to get out.  They transport back to the Mammon Room, and Schala uses the last of her power to send Magus, Marle, and Frog to land.
From the North Cape, the three witness the rise of the Black Omen into the sky, and mourn for Crono.  Magus reveals that he has sought to destroy Lavos for many years, but that is no longer a possibility, considering Lavos' great power.  Marle and Frog mention that if Crono can be found, they can defeat Lavos by combining their strengths, and Magus reveals the existence of an ancient artifact known as the Chrono Trigger that might help them.  He tells them it's in a dark world of the future, where evil is strongest, and they all immediately think of 2300 A.D.  Lucca lands and they scoot off towards the future, Magus remaining in the past.

Crono’s Dreamworld
Crono awakens and finds himself in the same moment as the morning of the Millennial Fair, though with slight variations.  He goes downstairs to find that the fair is starting that morning, and though he is confused, he starts to leave for the fair, stopping in the doorway.

2300 A.D.
The party singles out Death Peak, the mountain directly beneath the Black Omen, as the spot, and they land a short distance from the top, reaching the summit after finding a Lavos Spawn on the mountainside.  They then find the Chrono Trigger sitting in a tree on a cliff, and Marle goes up to the egg, calling out mentally to Crono.  

Crono’s Dreamworld
Crono asks his mother about what has happened to him, and then he realizes that he has the Rainbow Blade, a weapon that he was going to get that morning, thus proving his world to be a dream.  He hears Marle’s voice and then attacks his false mother, escaping his prison. 

2300 A.D.
A portal opens revealing the frozen moment in time, as Crono's body reanimates and floats to the ground.  Marle and Crono reunite, and the group shares some words, after which Crono spurs the group into action.

12,000 B.C.
Queen Zeal is absorbing energy from Lavos as Magus shows up to see and free his sister.  Schala, under Zeal’s control, brings down Magus’ defenses, and then Zeal captures his mind as well.  Shortly thereafter, Crono and the others enter the Black Omen.  Queen Zeal sees this and beckons them in, opening a stairway for them to get to her quickly.  They use it, and encounter the Queen, as well as Schala and Magus, who have been drugged senseless with Lavos' energy.  The Queen attacks, and attacks again, weakening the party.  Frog begins chanting, and awakens Magus with his words, who negates the Queen's attack and then destroys her.  Magus takes the stolen pendant and backs away from his mother, and the Queen reveals that killing her will only strengthen Lavos' power by freeing his reins.  Magus says this is the truth, and that the only way to reach Lavos now is by using a massive amount of energy, like that produced from a sacrifice.  Magus then gives his life to do so, as he and his sister and younger self all disappear, thus transporting the group to Lavos' final lair. 
Crono and the others battle the now-larger Lavos, finding that their weapons do no good against him.  Crono then asks the three to summon their energies and shoot them towards him when he gives the signal, as the red-haired warrior launches an assault on the huge creature that ends with his sword in the beast's mouth.  Crono shoots lightning at his blade, electrocuting Lavos, as the others join Crono's attack, and their powers combined destroy Lavos for good, his shell exploding, his body ruined.  The party transports back to the entrance of the Black Omen, Crono exhausted, and escape as the palace begins to crumble and explode.  They leap into the Epoch and zoom towards land as the Black Omen falls back into the sea, watching happily as the nightmare finally ends.  They then return to 1000 A.D.

1000 A.D.
Marle, Crono, and Lucca return to Guardia castle, and the King expresses great relief at Marle's return, welcoming her home.  The Chancellor accuses Marle and Crono of kidnapping, and just as they are about to be arrested (again) Marle sets the Chancellor straight by saying she ran away.  The Chancellor proposes a celebration, and the King mentions that it's the last night of the Millennial Fair.  Marle asks Crono, and Crono says it's a good idea, so that night, the two walk through the fairgrounds.  Marle kisses Crono on the cheek and runs up the steps to Leene's Bell, where they actually kiss, and everybody from that era is there to cheer for them.  Lucca beckons the two towards the main platform, and there waits Frog, ready to go home.  They all say their goodbyes, the Gate closes due to its purpose being accomplished, and the movie ends with Crono and Marle looking up into the sky, pondering the future.

THE END