The story takes place in the land of Sylvarant. Legend has it there once was a great mana tree, that produced prosperity to the land. However due to a rise in magi-technology which came into existence due to the limitless mana supplied by the Giant Kharlan Tree, a great war occurred between two opposing forces, and a hero named Mithos stopped the war, however due to the extensive amount of mana used during the war the tree withered and died, the legend states that Mithos the Hero died to take the place of the tree. Because of this, the goddess Martel mourned and fell into a "sleep". She told her angels that she must be woken up, or else the world will wither away. The angels gave birth to The Chosen of Mana (aka The Chosen One) who would go on a pilgrimage to each seal and regenerate the world.
In present day Sylvarant(4000 years later approximately), the world is in peril. Mana is lacking, causing food shortages and oppression by a technologically advanced group called Desians. The Desians consume much of the world's mana to create their technology. Colette was born as the new Chosen One. She lives in a small town called Iselia with her friends Genis & Lloyd. The story starts on Colette's sixteenth birthday, the day which she is supposed to receive an Oracle to start her quest for regeneration, but upon reaching the Temple near Iselia she and her friends discover the Desians are attempting to prevent her from completing world regeneration by taking her life. This partiular squadron of Desians are being led by a general named Botta. Genis & Lloyd try to stop them, but are unable - moments before the Desians can finish off the Genis, Lloyd and Colette a mysterious mercenary called Kratos arrives just in time to save them. Before entering the temple to receive the Orcale it is revealed that the Chosen must face a trial first. As the priests that were to attend the Chosen through this trial and her quest were killed by the Desians, Colette's grandmother hires Kratos as her protector. Colette - with the help of her compaions completes the trial where she proceeds to receive her oracle from Remiel and Angel of Cruxis. Remiel claims to be her real father - supposedly confirming the rumours that the Chosen One is the child of an Angel, and tells Colette to unlock 4 seals in 4 elemental temples (Fire, Water, Wind, Light) which will then unlock the route to theTower of Salvation, which was bestowed upon the world of Sylverant as Colette completed her trial and gained the title Chosen of Regeneration. She is to go to the Tower afterwards to complete the regeneration of the world and become an angel. Leaving the temple with Kratos to prepare for her journey, Genis and Lloyd are left to find their own way home. As Lloyd lives with his adopted father Dirk: a craftsmen dwalf. He immediately starts heading home for the day. Genis accompanies him claiming his is visiting a friend, but takes a different route half-way to Lloyd's woodland home. Worried for his friend's safety Lloyd follows Genis and discovers his young friend has been visiting one of the prisoners at the Iselia Human Ranch. Lloyd quickly befriends the old woman known as Marble, whom he becomes concerened about after learning she has an exphere on her. A strange little crystal which can improve the wearers stamina, speed, strength and magical abilities - Lloyd explains to both Marble and Genis that an exphere that doesn't have a keycrest and make a person sick. Lloyd suggests that he can get Dirk to make one for Marble, but they are unfortunately spotted by the Desian Guard and have to flee for fear of breaking the peace treaty between the Ranch and Iselia Village. (A treaty put in place to keep Colette safe from the Desians). After loosing the Desians, Lloyd continues home and is reprimanded when Dirk finds out he went to the Ranch - it is due to this Lloyd discovers a terrible truth. His mother was murdered by a band of Desians, because they were after the exphere that Lloyd now wears. After learning that his mother was killed by the Desians, Lloyd makes a decision to aid Colette in her journey. However as he arrives at Iselia - he finds Colette has already left without him, with Kratos and Raine (Genis' older sister). But the Desians from the Ranch start attacking the village before Lloyd can start to wonder why. A Desian Over-Lord known as Forcyetus approuches the villages and accuses Lloyd of breaking the peace treaty - and must be punished. A monsterous creature is brought forward for Lloyd to fight to the death. Genis loyally stands by his friend and they quickly defeat the monster. The monster to the surprise of the Desians then grabs ahold of Forcyetus- before telling Lloyd and Genis to run. It is revealed the monster is Marble in a mutated state. She then proceeds to self destruct injurying Forcyetus and causing the Desians to flee. Marble's exphere is all that is left. Genis keeps it as a memento of her.
Due to the damage caused by the Desians: Lloyd and Genis are banished as they are the intended targets for the Desians. Colette's grandmother instructs the two boys on where Colette was heading to first on her journey. The Fire Seal.
Lloyd and Genis, reach the desert town of Triet - where they discover they are now wanted fugitives of the Desians. They manage to avoid the Desians present in the town long enough to find out where the Fire Seal is, and by the fault where Colette it. However as they leave Triet. Genis and Lloyd are captured by the Desians. As they reach the Triet Desian Base - Genis is released from custody as the Desian Leader is only interested in Lloyd. As an unconscious Lloyd is dragged inside - Genis quickly runs off to get help.
Lloyd wakes up in the Desian Base and manages to escape his prison - while trying to sneak out of the base, he runs into the Desian Leader and Botta the General who had tried to kill Colette at the Iselia Temple. The two Desians quickly identity Lloyd due to his exphere - both give an indication that they know something of him. However the Desian Leader abrutly leaves the room before the Chosen's Group (Colette, Raine, Kratos and now Genis)come to Lloyd's rescue. The companions proceed to battle against Botta and over-power him - be he flees with his life. Raine gains her exphere from this battle.
Relucntantly Raine and Kratos allow Lloyd and Genis to join their party. Neither thinking this a journey for children - they proceed to the Fire Seal and after defeating its guardain releases the mana inside. Colette prays to the heavens at the seal as she was taught and Remiel appears again. He reveals the next seal is across the sea and the blesses Colette for her success so far - granting her angelic magical abilities and her angel wings. Remiel informs her the angelic transformation would not be without pain and wishes her luck in her trial. The trial in itself is revealed as they party leaves the Fire Temple. Colette falls ill for the night, but quickly recovers.
Lloyd and the others proceed through the Ossa Mountain Trail to reach to the seaside village of Izood. On they way the encounter an assassin known as Sheena. But she is quickly defeated, and flees claiming she will be back.
The Chosen's group travel on a fishing ship to the largest city in Slyverant: Palamacosta. Shortly after their arrival the nearby Desian overlord - Magnius has ordered the excuction of a shop keeper who refused to sell supplies to the Desians. Not willing to stand by and let an inoccent woman be hanged. Colette, Genis and Lloyd jump into action and quickly dispose of the guard saving the woman. Magnius is forced to flee. However the heroic efforts come back to haunt them as they discover a tour guide: the shop keepers daughter has been kidnaped by the Magnius' men. Despite the obvious trap - Colette refuses to the leave the tour guide: Chocolat to her fate. With Lloyd's support the attempt to rescue her. Although they fail in saving Chocolat. The Chosen's group strike a large blow to the Desian Strangelhold by destroying the Palamacosta Human Ranch. (After rescuing and evacuating the prisoners of course).
The group then after experiencing a odd experience of wash-tub boating. Reach Thorda Geaser: the location of the Water Seal. Their success continues in releasing the second seal, however Colette once again falls ill. Raine fasinated and concerned by this mysertious illness that strikes every time they release a seal dubs the sickness as Angel Toxicosis. Colette once again recovers and they make their way to the city of Asgard - a place that may hold the location of the Third Seal: The Air Seal. Much to their disappointment and possibly annoyance the City of Asgard isn't the location of the Third Seal, but a map to the third seal. They proceed to some ruins which the seal resides in and release the third seal. Before exiting the ruins however Sheena makes another attempt at Colette's life. After failing once again she exclaims her displeasure at not being able to defeat the group, and before fleeing remarks that Colette regenerating the world will mean her world's destruction. Confused the group leave the temple, only to have Colette faint due to her Angel Toxicosis. Its during this instance Lloyd makes and observation. Later that night he confront Colette about it - noting her injured hand and that she didn't react at all to the injury. Or the fact that she hasn't been eating or sleeping. Colette recluntantly admits the truth - her angel transformation is robbing her of her humanity. So far she has lost the need to sleep, eat and feel. Instead her eyesight has improved along with her hearing.
After this private discussion the group head towards the town of Luin, only to find it in ruin and its inhabitants gone. Its then they once again encounter Sheena - this time gravely injured, it is learnt she attempted to protect the town from the Desians. The villagers were harbouring escapees from the local ranch but were caught and they entire population was moved their as concequence for their actions. Lloyd and Colette convince Raine to heal Sheena, which she does so relucntantly. Lloyd's group agrees to help Sheena rescue the people of Luin and defeat the Desians of this area. At the Asgard Ranch - they influtrate the base through disguse and make their way to the prison area - however they are ambushed by the Desians and the Over Lord for this area -Kvar, . Kvar reveals to the horror of the party that expheres are parastic stones which are awakened after they absorb a life-force. In this case the human prisoners at the ranchs. After explaining this to the group Kvar then turns to Lloyd and demands he hand over his exphere, stating that it was apart of an important project which was to be presented to the Desian Leader : Lord Yggdrassil. The project was stolen (according to Kvar) by a female host body - revealed shortly after to be Lloyd's mother: Anna. A crime she paid for with her life - however Kvar revealed that it wasn't he who murdered Anna but Lloyd's father. When a crestless exphere was removed - it caused her mana (lifeforce) to go out of control mutating her body. (revealing what happent to Marble in Iselia). After which Lloyd's father killed Anna. Presently outnumbered the group retreat with Sheena's assistance. But return soon after to rescue the people of Luin and avenge Lloyd'a mother but defeating Kvar. Before the battle they arrive to find Kvar conversing via hologram to a woman named as Proynma. She makes a comment about Lloyd resembling someone. The battle ensues shortly after the conversation ends - the Chosen's group victorious. Kratos did an exceptional job of making sure he was dead after the team defeated him with Lloyd's assiatance.
Upon reaching the Tower of Mana it is discovered that Colette's humanity may be restored if healed with the power of a unicorn's horn. However the only known unicorn is trapped at the bottom of a lake. Sheena suggests that summoning Undine the Water Spirit to commune with the unicorn. It is then learned that the Seals are also the locations for the World's Summon Spirits. Having released the Water Seal - the companions are able to seek auidence with the Summon Spirit. Unfortuntly Sheena - who is a summonor is unable to make the pact to summon Undine due to Undine already having a pact with another: Mithos. Due some convienent knowledge on Kratos' part - Sheena requests the annuelment of the pact of Mithos. Undine then proceeds to attack the party. Naturally they prove their worth and gain her alligence. They return to Lake Umacy to free the unicorn - unfortunately despite the unicorn giving its horn up willingly to the party, it dies as its horn is its life-force. This saddens the younger members of the party, but they soldier onto the Tower of Mana once more to release the final sealEventually, they defeat the last of the seal guardains (shown in picture) and await Remiel to appear once more. However something odd happens this time. The Summon Spirit of Light - Luna appears and asks where Aska is stating she cannot make a pact with out him. The Summon Spirit then vanishes and Remiel appears - congratulating them of releasing the seals.
Upon leaving the tower once again Colette falls sick - this time the price of her further angel transformation is her voice. While waiting for Colette to recover Sheena admits her reasons for wanting to kill the Chosen. She explains that she comes from a world directly adjacent to Slyverant - Tethe'alla. The mana flow as they learn is like an hourglass. Tethe'alla is at present flourishing but is the Slyverant Journey of Regeneration is completed the mana in Tethe'alla will go to Slyverant causing Tethe'alla to go into decline. The only thing that exists in both worlds is the Tower of Salvation. Sheena having been in Slyverant for a while, is torn between saving Tethe'alla or Slyverant. The Suffering in Slyverant is almost too much for her to bear and she wishes to help them also. Colette suggests that they ask Remiel (tracing the words she wishes to speak on LLoyd's hand)if there was a way to save both worlds. Sheena then coldly remarks if there wasn't away she would have to kill Colette afterall. Colette indicates that she understands and adding she'll fight back because she loves Slyverant as much as Sheena loves her land - Tethe'alla.
The Group rest in Hima after booking a dragon flight to the Tower of Salvation. However Kratos is almost killed by an assassin as he converses with Noishe. Lloyd who followed him out manages to shout warning just in time.
(editing in process - please be patient)
When they finally made it to the Tower, Colette told Lloyd the truth about the pilgrimage: The Chosen Ones were meant to die in the Tower in order to save the world. The Angel Remiel reveals that he wasn't really Colettes father, but that it was a lie in order to motivate her. Colette is about to fully unlock her seal until Lloyd stops her and the team defeats Remiel. At this time, Kratos (Who went ahead of the group earlier) appears and tells them the truth about him. He was sent by a group called Cruxis to monitor Colette. Lloyd's group fights Kratos, but the leader of Cruxis, Yggdrasil stops them. Yggdrasil proved to be too strong for them. They would have died there if Botta and his men had not run in and provided an escape.
As Lloyd wakes up, a Desian walks in the room and demands their audience.When they go they find