Spoilers unmarked. Canon path assumed.
Thousands of years ago a giant magic tree called the Giant Kharlan Tree produced mana, the lifeblood of the land. Unfortunately a war caused the tree to wither, but it was stopped by a hero called Mithos.
The world of Sylvarant is a low-tech world where humans are being oppressed by technologically superior half-elves called Desians. The Desians kidnap humans and force them to do slave labor in concentration camp-like facilities called Human Ranches. Fortunately, a prophecy states that Cruxis (heaven) will designate a Chosen of Mana to go on the Journey of Regeneration (a pilgrimage to multiple holy sites) that ends with arriving at a magical tower called the Tower of Salvation and becoming an angel. This will awaken the Goddess Martel, causing mana to be restored to Sylvarant, the land to prosper, and the Desians to disappear. Multiple Chosen have embarked on this journey in the past.
Colette Brunel, the current Chosen, is issued the Cruxis Crystal (a magical gem from heaven) and sets out on her journey from the rural village of Iselia, accompanied by a mysterious mercenary, Kratos Aurion, and the local schoolteacher, a rare pure elf named Raine Sage. Her childhood friends Lloyd Irving (the village outsider because he is a human orphan raised by a dwarf) and Genis Sage (Raine’s younger brother) run into trouble with the local Desians and get exiled, eventually catching up to and joining Colette on her Journey. Along the way they are attacked by an assassin called Sheena Fujibayashi, who claims to be from another world called Tethe’alla.
It turns out Tethe’alla is another world that has its own Chosen system and the two worlds compete over a limited amount of mana. When Sylvarant prospers Tethe’alla falters and vice-versa. The group with Sheena in tow resolve to ask Cruxis to fix this system. When they arrive at the Tower of Salvation Cruxis reveals that the entire journey is a lie and it is the same organization as the Desians. Kratos reveals himself to be a high-ranking member of Cruxis and betrays the party, and they are nearly killed by Cruxis’ leader, Yggdrasil, before being rescued by a group called the Renegades. In the process Colette completes transforming into an angel and becomes completely unresponsive.
The Renegades are an organization of rebels who want to foil Cruxis’ goals, led by Yuan Ka-Fei. Like Cruxis they can travel between Tethe’alla and Sylvarant (using flying machines called Rheiards). The group is forced to escape the Renegades by traveling to Tethe’alla, where they hope to find medical aid for Colette. Tethe’alla is a relatively higher-tech world where half-elves are being oppressed by technologically superior humans. The group succeeds in gaining Tethe’alla’s leadership’s nominal aid. Along the way they meet Zelos Wilder (Tethe’alla’s Chosen) and Presea Combatir, a lumberjack.
Lloyd is able to cure Colette by making a magical charm called a Key Crest, but unfortunately Raine and Genis are discovered to be actually be half-elves (having disguised their lineage to avoid racism) and the group is forced to become fugitives. The group flees to Sheena’s home village of Mizuho, a village of ninjas that also face discrimination in Tethe’alla, and secure the aid of their spy network. Unfortunately Colette is kidnapped by Desians and imprisoned on a floating island. In order to rescue her the team steals Rheiards from the Renegades and gains the aid of the Summon Spirit of Lightning (a demigod), Volt. Along the way they meet a half-elf named Mithos and a convict named Regal. Genis and Mithos bond over their half-elven nature and become good friends.
Unsealing Volt causes Summon Spirits to be unsealed in both worlds, an event that has never happened before. It is revealed that the 8 elemental Summon Spirits were sealed to form a protective barrier around the Giant Kharlan Seed, which if allowed to germinate would grow into another Giant Kharlan Tree, solving Sylvarant and Tethe’alla’s mana problems. However the Seed has also been fused with the soul of the Goddess Martel, and if the seed germinates Martel will be destroyed. Cruxis’ goal is to resurrect the Goddess Martel and to that end has been genetically engineering Chosen to become the perfect vessel for her soul, as well as maintaining the competitive system to preserve what little mana remains (which maintains the Kharlan Seed’s life).
The party teams up with the Renegades to release the Summon Spirits and take control of a piece of magical artillery called the Mana Cannon to fire a massive amount of mana at the Giant Kharlan Seed, forcing it to germinate. The plan does not work as anticipated as the Giant Kharlan Seed goes out of control, causing massive destruction. The party is forced to infiltrate a Human Ranch to solve the problem but in the process discover that Colette is starting to literally crystallize.
To seek medical aid for Colette the group travels to the hidden village of the Elves, Heimdall. The party discovers that Colette’s disease is called Chronic Angelus Crystallus Inofficium, which once afflicted Martel herself, and that Martel was a half-elf, sister to the hero, Mithos Yggdrasil. Yggdrasil was once an idealistic youth and brought an end to the Kharlan War, where two opposing nations, Sylvarant and Tethe’alla, used so much mana in their warfare that the Giant Kharlan Tree withered. However, because he was a half-elf, he was victimized by racism, which actually killed Martel, turning Mithos into, ironically, a hateful racist. Since then he founded the organization of Cruxis and sought a way to both resurrect Martel and to fulfill her dying wish, which was for a world without racism.
In order to accomplish this, he invented an object called the Exsphere, a gem produced in Human Ranches that develops through inflicting pain on its host until it eventually traps their soul within the gem, putting them in a state of perpetual stasis. The Exsphere can then be equipped by another person, enhancing their combat abilities, but if equipped without taking the necessary precautions (using a Key Crest) the person can actually end up transforming into a monster.
A Cruxis Crystal is an advanced Exsphere that can transform its host into an angel. Yggdrasil used Cruxis Crystals to transform himself and his companions, Kratos and Yuan, into immortal angels, as well as to preserve Martel’s soul by allowing it to be consumed by a Cruxis Crystal combined with the Giant Kharlan Seed. He invented the Chosen system to create a soulless vessel that he could then dump Martel’s soul into, resurrecting his sister. He plans to also eliminate racism by forcing everybody to become "lifeless beings" (such as angels), thus eliminating racial differences.
Yggdrasil gained the power to do this through the Eternal Sword, an artifact that he was given by the Summon Spirit Origin. The Eternal Sword is a magic sword that can manipulate time and space, but unfortunately can only be wielded by half-elves. Yggdrasil used the Eternal Sword to split the world’s warring factions into two and restrict mana flow, preventing the development of the magical technology that caused the Giant Kharlan Tree to die in the first place. The party realizes that they cannot defeat Yggdrasil unless they can somehow separate him from the Eternal Sword.
Mithos reveals himself to be the same person as Mithos Yggdrasil and betrays the party. He also reveals that Kratos is Lloyd’s father before injuring Yuan and fleeing to his headquarters. The party sets out to take Yggdrasil down, but they are betrayed by Zelos, who reveals himself to be a triple agent who has been working for Cruxis, the Renegades, and the party simultaneously, trying to cast himself on the winning side. The party is captured but escapes from imprisonment to confront Yggdrasil, who is in the process of resurrecting Martel. Along the way Zelos returns, having faked his betrayal of the party to get the team into Cruxis’ headquarters, and to retrieve a material called Aionis, which when forged into a ring will allow a human to wield the Eternal Sword.note
Martel indeed does awaken but reveals that she does not approve of Yggdrasil’s methods before returning to the Kharlan Seed, shattering his sanity. He reinterprets her words as wishing to leave the planet behind and return to the homeland of the elves, Derris Kharlan, a giant comet made out of pure mana where Cruxis has made its base. Taking Martel (the Giant Kharlan Seed) with him would spell doom for both Sylvarant and Tethe’alla so the party strikes him down and escape the tower. Genis takes Yggdrasil’s Cruxis Crystal to remember his fallen friend.
The party now seeks to obtain possession of the Eternal Sword to reunite the worlds. It is revealed that only Kratos can release Origin’s seal, but if he does so he will die. Kratos duels Lloyd for closure and attempts to commit suicide by releasing Origin, but Yuan saves his life. However Yggdrasil is revealed to have survived in his Cruxis Crystal, possesses Colette, and flees to Derris Kharlan. The party pursues him, confront and defeat the demons of their pasts, and, after reuniting with Colette, strike down Yggdrasil once and for all. Lloyd uses the Eternal Sword to reunite the worlds and resurrect the Giant Kharlan Tree, which also reincarnates Martel as its new Guardian Spirit. Martel asks Lloyd to name the new tree. The credits roll before his answer is heard, but it is implied that Lloyd names the tree Yggdrasil (after the siblings), casting the game as a distant prequel to Tales of Phantasia.
The party then parts ways until the sequel.
For events after this, see Tales of Symphonia: Dawn of the New World and Tales of Phantasia.
