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The intro shows three people, a man in black (Panzer), a woman in red (Elise), and an older woman in a floating chair (Rilix) waiting on a cliff. A ship flies by, and the three people send spheres of energy at the ship. Panzer's and Rilix's inflict damage on the ship, causing it to fall; Elise's sphere of energy causes the Holy Ark in the ship to start glowing. Before the ship crashes, an escape pod shoots off into the distance.
The game opens with three soldiers standing outside a mine. They've been assigned to track down, and exterminate a ninja called Rodi. In addition to the soldiers already searching Desire Mine for Rodi, the renowned mercenary duo, Melody, a shaman, and Forte, a sorcerer, have been hired by the royal Enchantress, Rilix to find Rodi. Another mercenary, Arthur, a swordsman, (the playable character) has also been hired by Rilix to work with Melody and Forte to track Rodi down.
The three soldiers start speculating on what Rodi could have done to warrant the crown sending such a strong team after him. One of the soldiers mentions that he heard that Rodi was involved in a power struggle at the palace, to the confusion of another soldier, who heard rumours that the former Chancellor, and now Sage of the anti-Enchantress faction, Sabato, had hired a female paladin, Lisa, and a dragon warrior, Basso to find Rodi.
Arthur, Melody and Forte arrive. Forte asks how many people are in the mine, and both him and Melody are upset after one of the soldiers admits that Rodi is there alone, with Melody asking out loud why she and Forte needed to bring Arthur just for one person, and Forte mentioning that there'll be time to discuss splitting the pay for this job later.
The three of them enter the mine and easily find Rodi. Initially, Rodi welcomes them as the chosen ones to join him in spinning the threads of destiny, but his tone changes as soon as he realises there are three of them, and therefore must be the mercenaries hired by Rilix, rather than the pair sent by Sabato.
Rodi attacks, but once the fight is over (regardless of whether Arthur wins or loses) the ship that was shot down in the intro crashes through the ceiling, causing a cave-in that knocks all four through the floor, critically injuring them. Three spirits, two blue, one red emerge from the ship, but quickly disappear as a evil spirit approaches. The evil spirit bends over Melody, but before it can do anything, Forte kills it with a blaze spell, before falling to his knees. A second evil spirit possesses Forte, and floats away. As soon as the possessed Forte leaves, the three spirits return.
Arthur awakes in a dark corridor. As he walks along, he sees visions of Melody, Forte, Rodi, Panzer, Rilix and finally Galm, who wonders what the Creator wants from them, before telling Arthur that he has no desire to resurrect the Thousand-Year Kingdom.
A voice starts calling to Arthur, the dark corridors fade out. One of the three spirits appears and tells Arthur that the three of them (Arthur, Melody and Rodi) have been accidentally caught in the struggle between the forces of life and death. The Spirit goes on to say that all three are dying from their injuries sustained in the cave-in – Rodi has brain damage, resulting in amnesia. Melody's rib-cage is crushed, her lung pierced, and Arthur's condition is just as bad. The Spirit tells Arthur that the three Spirits feel responsible since it was their escape pod that caused the injuries, so to make amends, the Spirits will each possess Arthur, Melody and Rodi, which will eventually heal them.
The Spirit warns Arthur, Melody and Rodi that after they are imbued with the Spirit, they cannot be separated, even though they were enemies. All three agree, and the two blue Spirits possess Arthur and Rodi, with the red Spirit possessing Melody. They awake back in the mine, where they agree to work as a team, and Melody suggests that they try to find Forte.
Arthur, Melody and Rodi escape Desire Mine, and head to Desire Village. There they find that the border to Enrich, the capital, has been closed off. Rodi is thought to have been killed in the cave-in, and Forte returned to Enrich with the surviving soldiers immediately prior to the road being closed off.
Talking to the villagers also reveals that Desire Village used to be much more prosperous and populated than it is now; the mining trade used to bring in a lot of money, but after miners penetrated Godspeak, a shrine in the mountain, which was used as a place of worship by an ancient culture, more and more accidents occurred in the mine, and it was eventually shut down.
In the pub, the three meet Doyle, a Halfling determined to get to Enrich. Doyle muses about the possibility going through the nearby Forest of Confusion to reach Enrich, and invites Arthur to come along. Doyle tells Arthur to stay in the Inn for tonight, so they can make their full plans later. Lisa and Basso are also in the pub, having gotten to Desire after the cave-in, and subsequently stuck in the village after the border closing. Lisa and Basso have drawn the interest of the inn keeper, who wonders if they are a famed mercenary team consisting of a princess and a dragon.
Arthur leaves the pub, only to be confronted by Lisa and Basso, whom having seen Rodi, realise that Rodi is still alive. Lisa and Basso decide to use Rodi to search for something in Godspeak, and then turn Rodi in for the bounty. Just before a fight breaks out, the village elder interrupts, sternly demanding that the fight be delayed until the border gate opens. Lisa agrees and she and Basso peacefully return to the pub.
As agreed with Doyle, Arthur checks into the inn. Doyle shows up, and tells Arthur to head to the forest first, and Doyle will catch up with them later, arranging to meet at a graveyard deep in the forest if they don't meet up before. Arthur agrees, and first thing the next morning sets out for the forest.
Arthur, Melody and Rodi make their way to the graveyard in the forest, Doyle shows up again, this time calling Rodi “Boss”. Apparently Doyle used to be Rodi's right-hand man, though Rodi, still suffering from amnesia, doesn't remember Doyle at all. Doyle suddenly asks Arthur and Melody who they are, and Melody bluntly replies that she and Arthur were hired by Enrich to capture Rodi. Doyle panics; Rodi manages to calm him down, only for Doyle to go into a panic again when Rodi tells Doyle that he's going to Enrich castle. Giving up, Rodi opts to simply order Doyle to tell him about the secret path to Enrich. Unable to refuse a direct order from his boss, Doyle unlocks the grave that leads to the secret path, and gives Rodi a mask to wear, reasoning that Rodi is certain to be caught without some form of disguise. Doyle leaves, with a threat to Arthur and Melody that he'll always be watching.
In Enrich, the trio find the House of the Storytellers. The head Storyteller is more than happy to share some of his knowledge of history, and tells them about the Thousand-Year Kingdom, a place which initially flourished under the Innovators, but then the kingdom was taken over by a Vandal, and the Thousand-Year Kingdom became a place of fear, where the people had no dreams or hopes. The Kingdom was eventually destroyed by a power that came from beyond the sky, and the Vandal fled, to take refuge until the time the Thousand-Year Kingdom was reborn. The Storyteller also explains that Vandal possessed incredible physical strength and powerful magic along with a monstrous appearance. During their reign of the Thousand-Year Kingdom the Vandal repeatedly massacred his own people for no reason.
In the pub, Arthur finds Doyle already waiting. Doyle repeats his earlier warning that he'll always be watching, and walks out of the pub. There are two other mercenaries in the pub, one of them, Freddy, tells Arthur that they have nothing to do following Rodi's supposed demise in the cave-in, and are considering going treasure hunting in the mansion at the edge of town. In addition to the mercenaries, there's an older man, whom darkly warns Arthur that the owner of the mansion has lived there for several centuries drinking human blood; he is certain the mercenaries will pay if they do go out to the mansion.
Outside the pub, Elise approaches, and knocks out a dog with a bat. Both Melody and Rodi prepare to fight, but Elise teleports onto the roof of the pub, and then disappears. Rodi warns that Elise's magic doesn't feel like natural magic at all.
Arthur, Melody and Rodi go to Enrich Castle, and enter the throne room, where the King, Rilix and Forte are waiting. The King summons them forward, then immediately asks if Arthur is certain Rodi is dead. Arthur remains silent, and Rilix reveals that she's fully aware Rodi is travelling with Arthur. Rodi interrupts with a spell that forces the evil spirits possessing both the King and Forte to reveal themselves. Rilix points out that attacking the evil spirits will kill the King and Forte and correctly reasons that the trio won't fight under those conditions. She drops Arthur, Melody and Rodi into the dungeon instead.
In the dungeon, Melody and Rodi discuss their options, until Doyle, standing upside down on the roof of their cell interrupts to unlock the door (and take the mask back from Rodi), before leaving with instructions on how to get out of the castle via the waterways.
In the waterways, the trio meet Sabato, who tells them that a crisis is coming, and to avert it, the first thing to do, is to go to Aborigine Mansion and meet with Galm. Sabato also tells them that it was Galm whom told Sabato to send Rodi to Godspeak. Sabato warns that even though Galm supports Sabato, Galm has no need to cooperate with them if he doesn't wish to, and as part of a test to ensure Arthur, Melody and Rodi are worth the risks Galm will be taking in providing aid, the trio will first need to find the key to the mansion, located in the waterway, as a test.
Arthur finds the key, and returns to Enrich town. There, he finds a young Julian sitting outside the pub. Julian offers Arthur the most important thing he owns if Arthur can find his dad, who has been missing after going to the mansion.
Arthur also encounters a young girl, who wants to talk about Elise. She tells Arthur various rumours about Elise, one of them being that Panzer is Elises' lover. While the girl is talking, Elise appears, and raises her hand towards the girl, who falls to the ground, flesh pulsating, body distorted, before the girl disappears.
The head Storyteller tells Arthur that corruption is the one thing that could bring about the rebirth of the Thousand-Year Kingdom, but only the Holy Ark, a vessel that absorbs and contains corruption is capable of achieving this. There is a legend that if the Holy Ark is ever opened, the world will be engulfed in horror as the corruption is released, and eventually everything will disappear with the Ark.
Arthur sets off for the Aborigine Mansion, eventually running into an injured Basso. Basso tells Arthur that he and Lisa followed Arthur through the forest to Enrich, but couldn't find out what had happened to Arthur after Arthur went into the castle. As a result, Lisa and Basso decided to split up, with Lisa trying to sneak into the castle, while Basso investigated the mansion. Basso couldn't get into the mansion through the front door, as he didn't have a key, but did find some catacombs, so decided to search those, only to be attacked by Galm. Upon hearing that Arthur intends to see Galm, Basso requests to go with the trio, as Galm is the first thing that has ever caused Basso to feel fear.
Continuing on, Arthur finally finds Galm. Galm tells Arthur, Melody and Rodi that they are the three destined to stop the revival of the Thousand-Year Kingdom. Melody and Rodi are initially sceptical of trusting a Vandal; Galm assures them that he himself has no interest or desire to see the Thousand-Year Kingdom rebuilt, he only wants his peace and freedom. Galm also tells them that Sabato, searching for answers about the Thousand-Year Kingdom, was the one that awoke Galm, and Galm sees this as a good chance to repay Sabato for awakening him, and that's why Galm agreed to help.
Galm instructs Arthur to go to three ancient shrines, one in the South, one in the West and one in the East. There is a sacred treasure in each that will be needed to stop the revival of the Thousand-Year Kingdom, and the South Shrine holds the Sacred Sword that will allow Arthur to fight the evil spirits without harming the King or Forte. Galm gives them a key that will allow them to get through the South Shrine, and advises Arthur to find the tower of the people that fled beyond the wall paintings when the Thousand-Year Kingdom fell once he has all three sacred treasures.
Galm leaves, and Basso comes forward saying that now he realises his opponent was a Vandal, it's understandable that Basso lost to Galm, though Basso still vows to repay Galm someday. Basso leaves the party to find Lisa, but also assures the trio that he understands now that they are on a vital mission; he and Lisa won't attempt to interfere again. Before Basso leaves, Melody uneasily tells Basso to come find them if anything happens.
The trio start to make their way to the South Shrine via a Mountain Cave, but right at the entrance to the cave they encounter Basso again, who gravely informs them that Lisa disappeared after sneaking into the castle. Melody and Rodi worry that Lisa might have run into Rilix; Lisa's no match for a Vandal, and as Lisa was hired by Sabato, it's likely that Rilix would consider Lisa an enemy. Melody is inclined to run back to the castle to try save Lisa, but Rodi points out that Lisa's possible predicament is only another reason to rush onto the South Shrine. Basso agrees with Rodi and joins the party again.
The quartet make their way through the cave to the Far East Village, Rodi's home town where everyone studies Ninjutsu. They meet with Rodi's father, the Lord of the village, who tells Arthur that the Spirit is supposedly the origin of all power, if one can become one with it, that person will inherit abilities beyond other people. The Lord urges Arthur to follow Galm's advice and retrieve the Sacred Sword from the South Shrine while he has someone investigate Enrich Castle.
Arthur manages to get the Sacred Sword and returns to Far East Village. The Lord, true to his word, sent Doyle out to check out Enrich Castle while Arthur was in the South Shrine; apparently Rilix has sealed off the castle gates. The Lord summons Doyle to discuss potential other options to getting into the castle, only for an injured Doyle to appear out of nowhere, before throwing a dagger at an invisible Panzer. Panzer asks the Lord why he doesn't let the world know that Ninjas are supreme; the Lord replies that there's more to fighting when it comes to protecting the lives and well-being of the people living in a land. Panzer drops the subject, and instead demands that Arthur hand over the Sacred Sword. The Lord refuses in Arthur's stead, stating that maybe it's because of what Panzer really is that has made Panzer join Rilix. Enraged at the insinuation, Panzer starts to summon some magic, but stops as soon as Akane, Rodi's sister, appears. Akane tells Panzer that he'll have to go through her to get to the Lord, and Panzer, who thinks of Akane as a sister himself, backs down and leaves.
It turns out that Akane was on a mission to see if a passage from the waterway to the throne room was still open; it is, and Akane joins the group, under the reasoning that it will be harder for Panzer to attack if Akane is with Arthur.
The Team successfully make their way to the Enrich throne room, where the King and Forte are slumped on the ground, Rilix hovering above them. Rilix gleefully tells the party that she allowed them to escape, so she could trap the Spirits inside Arthur, Melody and Rodi later. With that, she summons the evil spirits possessing the King and Forte to fight the party while she sits back and watches. The Party defeat the two evil spirits, and Sabato teleports into the room, tells Arthur to use the Sacred Sword on the evil spirits, which Arthur does, separating them from their hosts. Rilix decides to enter the fray herself to fight the party, and Sabato teleports out before the battle begins.
The Party defeat Rilix, but before they can kill her, Panzer shows up, tells the party that he and Rilix will be heading to Godspeak to begin the ceremony of rebirth for the Thousand-Year Kingdom, and takes off with Rilix. Sabato shows up again, and congratulates the party. An official celebration is held throughout Enrich.
The next morning, the party is summoned to the throne room again. The King and Forte thank the party for freeing them from the control of the evil spirits. Sabato explains that although Rilix is a Vandal, she is a very weak one, unlike, Elise, Rilix's sister. Sabato also explains that Desire Mine has been blocked off, leaving them with no alternative, but to have the powers of the Spirits inhabiting Arthur, Melody and Rodi released.
Sabato provides a little more information on the Spirits; they are a source of power given to selected mortals by the Creator. This used to be a frequent occurrence, but after the old kingdom collapsed, the Spirits disappeared for a thousand years, when they reappeared with the Holy Ark. From passed down legends and murals found underneath the castle, Sabato realised that three heroes, two male, one female, would be imbued by the Spirits, and would be the ones to battle the Vandal's, the only hope to prevent the rise of the Thousand-Year Kingdom again. A search was launched to find these three people, but ultimately, Rodi was the only one selected, though Sabato thought that Lisa and Basso could be the other two.
Sabato and the King believe that the room with the murals also contains a gateway to another world, which will only open with the three sacred treasures. In that other world in the Tower of Illusion is a priest with the ability to release the Spirit's power, something that no one in Enrich can do.
Before the party set off for the next shrine, Forte rather begrudgingly joins the party to repay his debt.
In Enrich town, a man tells the party that someone went to the mansion to look for the treasure-hunting mercenaries, only to find bits of flesh (that someone had been feeding on) and clothing strewn everywhere. Julian is still sitting outside the pub; a friend of his father has been taking care of Julian since his father disappeared, but now the friend has told Julian that they have to leave Enrich without his father. Julian says that he is afraid of the friend, but has to do what the friend says. Julian really wants to cry, but he won't let himself do that since his father used to tell him that he should never cry, otherwise he would never become stronger. Inside the pub, the friend of the father vows that he will raise Julian to be the best mercenary in the world, in memory of his father. The mother of the girl attacked by Elise is frantically searching for her daughter, having no idea what happened to her. The Storytellers now start talking about the Apostle of Light, a priest that can release the power of a Child of Light, a source of power that inherits a human body, and grows with it's host, physically and mentally.
From information gathered in both Enrich and Far East Village at this time, it's revealed that Galm is Panzer's father – he abducted a girl from Enrich more than twenty years ago and took her to the mansion. The girl survived the ordeal, and returned to Enrich, but when she discovered she was pregnant, she left Enrich and ended up in Far East Village. The journey had weakened her so much that she didn't survive the birth, but refused to sacrifice Panzer's life to save her own. Panzer was raised by the Lord of the Far East Village, and came to see Akane as a sister, but developed a strong rivalry with Rodi. As Panzer grew up, he became prone to violent outbursts, and scared of the possibility of hurting Akane one day, Panzer left the village.
Doyle, for some reason, is pretending to be a tree in Desire Village. If Arthur finds and talks to him, Doyle, the only optional member of the party, joins up.
With the Sacred Sword, the party can now open the West Shrine seal. They do so, and at the end of the West Shrine, find Galm with Lisa. Apparently, Galm found Lisa just as Elise was about to kill her, and on a whim, decided to save Lisa. Galm tells the party that he'll be watching and leaves. Lisa explains that she followed Arthur, Melody and Rodi into the castle, but then ran into Elise, and after that she doesn't remember anything – it's not mentioned in the game, but an official supplementary material reveals that Galm impregnated Lisa at this time – Lisa also says that Galm told her about Arthur, Melody and Rodi's destiny; Lisa's own kingdom fell into chaos, and she vowed she would never allow that to happen again, lamenting that if people like Arthur had been around at the time, the people of her kingdom would have risen up against their oppressors, and she readily agrees to help out.
The Party pick up the Sacred Mirror, and head off to the East Shrine, where they find the Holy Pendant. They return to Enrich Castle, and pass through the gateway to the world beyond the paintings. The party finds the Tower of Illusion, where the High Priest, the Apostle of Light, awaits, and Mirage Village, where time never passes.
In Mirage Village, the party finds out that the ceremony to release the Spirit's power is called Evolution. After Evolution, only time will tell if a host of the Spirit will become an Innovator, or a Vandal.
The Party ascend the Tower of Illusion, and meet the High Priest. Before the High Priest starts the Evolution ceremony, he relates a bit of history; The Thousand-Year Kingdom was one ruled by heroes, spirit hosting Innovators, and the public adored them as the pillars of the kingdom. However, over time, the people forgot that their happiness was due to the Innovators, and started to take their happy, wealthy lifestyles for granted. As a result, the kingdom, built on the ideals of justice and peace, started to become corrupt, and the darker side of the Spirit was invoked, transforming the Innovators, dismayed over what was happening to the people of the kingdom, into the first Vandals. The High Priest warns the party that the Spirit is the origin of all power, and a test from the Creator, whom wishes to see how well a society can handle prosperity; if the society fails the test, the Creator will destroy that society and culture, as the Creator did with the Thousand-Year Kingdom. The High Priest continues that his honest preference would be not to conduct the Evolution ceremony, but the Vandals attempting to raise the Thousand-Year Kingdom have left him with no choice.
The Evolution Ceremony is performing, turning Arthur, Melody and Rodi into Innovators. The High Priest warns that the change will be gradual, although all three have gained new spells immediately after the ceremony. During the ceremony, the High Priest also learnt that all three have a very weak connection with their Spirits, as the Spirits wish to return to the Holy Ark. Arthur's new spell (Inferno) is strong enough to shatter the barrier to Desire Mine and Godspeak that Rilix and Panzer erected, the High Priest tells the party to go to the Holy Ark and find out for themselves what the Spirits want.
The Party return to Enrich, much to the confusion of Sabato and the King, as to their perception, the party have only just left to enter the world beyond the paintings.
The Team return to Desire Mine, breaking the barrier, and arrive at Godspeak, where Rilix and Panzer are standing in front of the Holy Ark. Rilix decides to fight the party while Panzer continues to open the Ark, and starts to summon some vampires to help her fight. Elise arrives, asking if she can help in Panzer's stead, and enhances Rilix's vampires.
The Party defeat Rilix, this time killing her and Panzer seems close to giving up the plan to open the Ark. Elise calls him out on it, and Panzer questions her motives, like Galm, Elise has no interest in the Thousand-Year Kingdom. Elise announces that she couldn't just stand by after Rilix was killed, and promises to help open the Ark to fulfil Rilix's last wish. Elise starts to use her magic on the Ark, but Galm appears and shoots a sphere at Elise, stopping her. Galm tries to sympathise with Elise over Rilix's death, but Elise casually admits she's not upset at all, a small part of it is because Panzer used to be her lover, but mainly, she just wants the team to suffer and enjoy herself in the process.
Panzer demands to know why Galm is there, reminding Galm that although Galm said he wouldn't help with the plan to revive the Thousand-Year Kingdom, Galm also promised not to interfere. Galm agrees, then goads Panzer into jumping into the Ark, which has just started to open. Panzer takes the bait, and emerges as the final boss.
Once Panzer is dead, one of the Spirits talks to Arthur directly, saying that the Spirits will return to the ship with the Holy Ark. Apparently, the Spirits were contaminated with evil when they possessed Arthur, Melody and Rodi, but the ship that is coming to collect the Ark will cleanse them of the evil. Two of the Spirits leave their hosts, and return to the Ark.
Elise reappears, and calmly asks Galm if everything went to plan. Galm isn't sure, he wasn't anticipating that two of the Spirits would leave, but Elise reasons that the remaining Spirit will disrupt the balance, and that should be enough to finally understand the Creator's plan. Galm agrees, but bemoans the cost of the price to find out why the Creator brought the Spirits to the world. Galm wonders if people can really use the power of the Spirit for peace, given that most seem to have an innate desire for power, and wonders if this too, is part of the Creator's plan. Galm leaves, warning Elise that they'll be absorbed by the Ark, and unable to return if they linger any longer. Elise stays for a moment longer, asking the team if they now understand what Galm's plan was, and is looking forward to finding out which the three (Arthur, Melody or Rodi) still has their Spirit. (It never was officially confirmed who kept their Spirit.) Elise leaves, and the two Spirits that left bid farewell to the party, promising that they'll always remember their journey together.
The party return to Enrich, and each are given a large reward, as well as an offer of permanent employment in the army. They go to the pub to celebrate, but Arthur leaves before the rest of the team, and goes to the throne room alone. Arthur officially rejects the offer made to him (Defence Minister) deciding that he values his freedom more. Sabato and the King reluctantly accept Arthur's decision, and promise that he'll always have a home in Enrich.
In town, Arthur finds Akane, crying over Panzer's death. Rodi is also outside, just outside the pub, feeling a little overwhelmed by the celebrations inside. Julian is nowhere to be found, the mother of the girl attacked by Elise is still searching for her daughter, and finds no joy in the restored peace.
The rest of the party is inside the pub. Melody is content, and can't understand why Arthur and Rodi aren't sharing that feeling, given that they've defeated the Vandals, and have been offered good jobs. Forte intends to go his own way, now he feels he has repaid his debt to Arthur. Basso and Lisa have also both decided against joining the Enrich army, as they feel they have their own destiny. Lisa almost asks Arthur if he wants to join her and Basso, but retracts the offer at the last minute, and simply wishes Arthur luck. Doyle is simply overwhelmed by being in the spotlight.
Arthur leaves the pub, and Rodi calls out to him. Rodi asks what Arthur is planning to do now, correctly guessing that Arthur doesn't really have a plan going forward. Rodi is concerned that no one knows who still has the Spirit, and resigns himself to simply waiting to find that out. Rodi wishes Arthur well, then disappears.
Arthur leaves Enrich for the final time, and the game ends.