Many Years Ago:

• The great archmage Noah is about to expire. He divides his legacy among his three students. To Doga he gives the realm of magic, to Unei the realm of dreams, and to Xande the realm of humans. However, Xande despises his role and yearns to rule all three worlds. To that extent, he summons the Cloud of Darkness out of the World of Darkness to do his bidding.
• Another student, Owen, decides to create a Floating Continent. He builds a tower to control it, and appoints his son Desch to watch over the tower. However, the tower is taken over by monsters, and Desch is thrown out, losing his memory in the catastrophe.

Present:

• Four young boys are lost in the Altar Cave, near the city of Ur (in FF3DS, only Luneth becomes lost in the cave). They come upon a large Crystal. The Water Crystal tells them of Xande's plans, and decides that they are the four legendary warriors destined to defeat Xande and restore order. It bestows legendary Job classes upon the four.
• They bid farewell to their adoptive father and mother, Topapa and Nina, and start on their journey.
• They are blocked passage to the outside world by a large boulder outside of the city of Kazus. Upon entering Kazus they discover that everyone inside has been transformed into shadows. Jinn, the being responsible for this, has locked himself away in the Sealed Cave. Cid, an eccentric old man who owns an airship, lends it to the youths to allow them to reach the Cave.
• The youths meet Princess Sara of Castle Sasune inside the Cave. She has the Mythril Ring needed to seal Jinn, and she tags along with them. They succeed in defeating Jinn and sealing him inside the ring. Sara takes them to Castle Sasune, where she tosses the ring into a fountain to break the spell. The king, Sara's father, expresses his support for the Light Warriors' mission and lends them a canoe.
• Cid enlists the help of Takka, a blacksmith in Kazus, to affix his airship with a battering ram. Using the ram, they destroy the boulder blocking the path outwards. However, the airship is destroyed.
• The first town the youths come across is Canaan, where Cid's home is; Cid takes his leave of them. They continue east to a large mountain which turns out to be the home of Bahamut, king of dragons. Upon their intrusion, he takes them to his nest. They unexpectedly meet a mysterious man named Desch with amnesia who is in the same predicament. Desch encourages the party to run away from the monster; they succeed in doing so, jump out of the nest, and land in the Healing Copse. Desch gives them the useful Mini spell, used for shrinking people's sizes, and tags along with them in the hopes of discovering who he is.
• Trying the spell out, they discover a town of gnomes called Tozas. After giving a sick man an Antidote, he opens a path out to the real world again. They take the Tozas Tunnel and exit near the Viking's Cove. They discover that the Vikings are paralyzed by a sea monster named Nepto. They lend the Light Warriors their ship in hopes of destroying the beast. The Warriors enter Nepto's Shrine and discover that a ruby eye from a statue of Nepto has been stolen by a giant rat. After restoring the eye, Nepto calms the seas and rewards them by giving them the Water Fang, one of four keys.
• The Warriors enter Gulgan Gulch, a place populated with one-eyed prophets. They are given the Toad spell for use in turning themselves into frogs. The Gulgans advise them to use it when entering the Tower of Owen, where Desch will learn of his destiny.
• After defeating the monster controlling the Tower, Desch learns that he is the son of Owen and it is his responsibility to watch over the tower. A fire breaks out when the monster is defeated, and Desch throws himself in to quench it and stabilize the tower and the Floating Continent.
• A new passage opens up via sea to the Dwarven Hollows, where it seems the ones of the dwarves' two treasured Horns has gone missing, stolen by a thief named Gutsco, who fled to an underground lake. The Warriors track him down, defeat him, and regain the horn. However, he hides in their shadows and follows them back to the Dwarven Hollows, where he steals both horns! He repairs to the Molten Cave, where the Horns and the Fire Crystal allow him to transform into a Salamander. The Warriors find and defeat him again, and free the Fire Crystal.
• Upon hearing rumors of the town of Tokkul, the Warriors travel there only to find it deserted. They are taken to the floating Castle Hein, where the evil sorcerer Hein has imprisoned the people of Tokkul and Castle Argus. Castle Hein is actually a floating tree called Yggdrasil, which used to rule the fairies in the Living Forest until Hein captured it. The Warriors succeed in defeating Hein and restoring both Tokkul and the Living Forest; the grateful fairies give them the second key, the Water Fang.
• The newly released king of Castle Argus, in gratitude, gives the Warriors a Time Gear. Cid in Canaan uses it to allow their ship, the Enterprise, to fly! They find that they are on a Floating Continent; the entire real world is beyond the clouds.
• The real world is almost completely submerged by water. They find a lone island with a shipwreck on it. A wounded woman lies inside. The Warriors heal her with a Potion and she introduces herself as Aria, Maiden of Water. She goes with them to another island housing the Temple of Water. She finds shards of the Water Crystal in here and urges them to take her to the nearby Water Cave so she can restore the Crystal. They do so, but the effort drains Aria completely and she passes away. The rest of the world is now revealed.
• The Warriors land in a town called Amur, but a man named Goldor has chained up their airship! Goldor lives across a deadly swamp which can only be reached with special shoes found in the Amur sewers. The Warriors come across four old men who think *they're* the Light Warriors, funnily enough. Jiru, the elder of Amur, will unlock the sewers. The Warriors rescue the foolish old men from a pack of Goblins, and the old men realize the truth. They find an old lady named Delilah who keeps the shoes. She's reluctant to give them away, but the four old men suddenly show up and save the day, and Delilah gives them the shoes.
• The Warriors travel to Goldor's Mansion, which is made entirely of gold thanks to a special Gold Crystal. After they defeat Goldor, however, he destroys the Crystal. Their ship is released, though.
• When flying their airship over the large city of Saronia, the Warriors are shot out of the air by a stray bullet. It seems Saronia is fighting with itself. The reason is that Gigameth, the chancellor to King Gorn, has been controlling him. He banished Gorn's son, Alus, from the castle. The Warriors find Alus in a bar and he begs them to help him back to his home.
• They find the legendary Dragoon Tower in Saronia, which houses equipment from the ancient Dragoons. Since Gigameth is only vulnerable to Dragoons, the Warriors loot the place and change into Dragoons. King Gorn invites them into the castle and gives them a room, but comes in the middle of the night to kill Alus at the bequest of Gigameth. However, before he can, the king instead stabs himself. Gigameth transforms into a giant bird, Garuda, which the Light Warriors dispatch with the Dragoons' skills.
• The freed people of Saronia Castle replace the Warriors' airship with a faster version, the Nautilus. They battle the winds of Doga's continent to reach his house, where his Moogles attempt to stop them. Doga allows them in, though, and he fills them in on the past story involving Zande. He accompanies them through the Cave of the Circle to reach an ancient circle, which allows Doga to give the Nautilus the ability to submerge in water. The Cave collapses, but Doga warps the Warriors out just in time. He tells them to find the Lute, which will wake the sleeping Unei.
• The Lute, hidden in the underwater Temple of Time, is retrieved by the Warriors and used to awaken Unei, who gives them the third key, the Wind Fang. Unei takes the Warriors to the Ancient Ruins, at the end of which is the enormous Airship Invincible. She gives it to them to help them in their quest. The Invincible helps them reach the Cave of Shadows, a huge cavern. At the end is the Earth Fang.
• Having all four Fangs allows the Warriors to enter a continent guarded by the four Statues of the Quest. They reach an old and enormous structure called the Ancient's Maze. At the start lies the final Crystal, Earth, which they liberate. However, the way forward to Xande's lair is locked. They return to Doga's Manor.
• Doga and Unei take them to Doga's Grotto, at the end of which Doga and Unei demand that the Light Warriors fight and kill them. They are reluctant to do so, but are attacked by the two mages. They defeat them, and from the energy expended from their demises they receive the keys to Eureka, the Forbidden Land and the Syrcus Tower.
• They return to the Ancient's Maze. After navigating it, they reach the first floor of the Syrcus Tower. Eureka, which is reachable via a portal, holds all the ultimate weapons and job classes, and reaches seven floors down. The Syrcus Tower extends upwards. At the last floor, Xande confronts the Light Warriors and paralyzes them. But Doga and Unei summon five souls (Cid, Alus, Sara, Desch, and one of the old men from Amur) to help them. The Warriors defeat Xande but the Cloud of Darkness he summoned still exists. The Cloud attacks them, but they are revived by the five souls. They follow the Cloud of Darkness into the World of Darkness.
• They come across four Dark Crystals, each of which holds a Dark Warrior who helps them in their battle against the Cloud of Darkness, which they ultimately destroy.

Side Quests:

• Cid's wife in Canaan is deathly ill. The youths heal her with an Elixir they find dropped by a passing magician and are granted access to Cid's treasure room.
• Cities with interesting shops include the Ancients' Village on the Floating Continent, Gysahl on the Floating Continent (it makes Magic Keys), Falgabard (village of Magic Knights/Dark Knights), Replito (village of Summoners), Duster (village of Bards and Geomancers), and Doga's Village (where you can buy any magic you want).
• The Undersea Cave is replete with treasure. The Saronia Catacombs also has a lot of treasure, and at the end resides the Odin summon. Lake Dohr and Bahamut's Cave in the Floating Continent are home to the Leviathan and Bahamut summons, respectively.