A great witch, Anise, from a realm yet unknown brought darkness to the world. She was defeated by the guardians of the great tree.
But legend tells that her darkness and curse seeped through and spread over to many other worlds. When the world was still covered in darkness, the Mana Goddess used the Sword of Mana to defeat the benevodons that would lead the world to doom… Then sealed them into eight stones.
After completing her creation, the Mana Goddess turned herself into a large, wizened tree.
It is told that the Mana Tree and the sword continue to watch the world from the forbidden Sanctuary.

Ferolia, the kingdom of Beastmen, is reported to be planning a war on humans. Roget and the reconnaissance crew had left Pedda to see if there was any truth to this rumour. But a sudden raid by the Beastmen has sent the party’s ship crashing into the woods. To make matters even worse, the ship’s carrier, the Splendere, has abandoned them amidst the chaos. Will the crew of five scouts succeed in their mission? Will they even make it out alive…?

Roget has fended off the initial threat by learning the Nightswan’s abilities and summoning ally units. But the crew is soon surrounded by Ferolian troops led by their king, Gauser. The crew is then shocked to hear that Peddan forces have commenced an attack on the Beastmen’s kingdom. The Nightswan crew decide to head for Lowenburg in order to uncover the truth, not knowing what awaits them…

Pedda’s attack on the kingdom of Beastmen was true! In charge of the attack is General Baxilios. The crew learns of two enigmas: Esina’s black mirror and Operation Psi. Now labeled as traitors, the crew’s lives are in danger. Narrowly rescued by Gauser, Roget and crew hurryr to Pedda’s next target, a village of Beastmen…

As the crew arrives at Mintas, Peddan troops press Gauser to surrender. The king of Beastmen refuses to comply. Peddan soldiers threaten violence as they mercilessly set fire to the village. After fighting the enemy and rescuing the villagers, Gauser decides to leave the burned-down village to accompany Roget and crew and inform other states about Pedda’s atrocities. They must reach Laurent, the impregnable aerial citadel and next likely target, to warn and prepare against Pedda’s looming invasion…

Roget and the crew try to convince Laurent to take action, but to no avail. Meanwhile, Peddan forces arrive earlier than expected. The Peddans had formed a hasty alliance with Nevarl of the Burning Sands. After a bloody battle, Laurent falls into the hands of the Peddan-Nevarlan alliance. Laurent’s matriarch, Galura, is murdered; her daughter, Minerva, is taken hostage. Powerless and dejected, Roget and crew head for Wendel, the sacred capital, to ask for help from the Priest of Light…

In Wendel, Roget and crew heard about defectors in the Burning Sands of Nevarl. Joined by Belgar, the Oracle of Shadows, the crew heads for the desert land. There thye meet Falcon, a Nevarlan secret agent, who joins the party. They also encounter a Mana Stone, thus successfully employing the powers of the elemental spirit and the benevodon. Now armed with a chance of fighting back against the Peddan forces, Roget and crew head back to Wendel…

Roget and the crew of the Nightswan head for Valsena, the kingdom of green fields, to prevent further incursions by the Peddan-Nevarlan allied forces. Standing in their way, however, is Juhani, brother of Roget’s fiancée. Juhani calls Roget a traitor and cannot be reasoned with. Roget has no choice by to fight a dear friend. At the end of the fight, Juhani falls down a ravine. A heartbroken Roget must continue on to Valsena…

Prince Richard of Valsena leads the battle on Molebear Moors. Leading the fight against Roget and Richard is Celestan, who seems to have a history with Yurchael. A victorious Roget and crew are joined by Gnome, the spirit of the earth. But while it momentarily looks as though Peddan forces are in retreat, they resume their advance assisted by dragons. The showdown must take place in Castle Valsena…

The battle rages on between the Altenish-Valsenan intercontinental alliance and the Peddan-Nevarlan forces who are supported by powerful dragons. The victory for the intercontinental alliance is fleeting; Castle Valsena falls under the crushing power of General Baxilios. Operation Psi continues to move forward as a third Esina’s mirror starts to shine. Roget and crew are forced to retreat to Altena, the kingdom of sorcery…

Peddan forces are now advancing on Altenish soil. The Queen of Altena casts magic powers of the Mana Goddess to freeze Peddan troops in their tracks. But when General Baxilios arrives and Esina’s mirror unleashes its power, the Mana Goddess’ spell is broken. Peddan troops rush into the castle. Princess Valda and the Nightswan crew are persuaded to make their escape as the Queen of Altena accepts her own fate…

A relentless prusuit by Peddan forces brings the Nightswan to Frostbite Fields. Roget and crew narroly survive as the forces are beaten back by Valda’s wrathful sorcery. But as they raise their eyes to the light that emanates from Esina’s mirror in Castle Altena, they face the fact that five out of the six major powers of the land have now fallen under Pedda’s rule. The Nightswan heads for the last surviving state, Wendel…

At Wendel, the Priest of Light tells the crew that the only way to counter the Peddan forces would be to gain the elemental spirits as allies. While seeking the Mana Stone of light at the Shimmering Ruins, the crew encounters Inath, the king of Pedda. Inath talks to Roget as though they have known each other for a long time. Inath invites Roget to join his side; Roget refuses. With the help of the spirit of light, the crew continues on a search for the remaining mana Stones…

Roget and crew arrive at the Woods of Wandara in their ongoing search for Mana Stones. But Flamekahn, Falcon’s father, stands in their way. Flamekahn allies himself with Pedda out of love for his people. Falcon seeks coexistence and co-prosperity with other nations. The fight between father and daughter seems as though it would end with the daughter’s defeat, when the Mana Stone of wood appears. Flamekahn leaves without finishing the fight. The party continues on into Altenish territory in search of Mana Stones…

A battle ensues with Celestan, who was waiting for the crew in the Labyrinth of Ice. Awakened from its long sleep is not only the Mana Stone of water, but also the Luzio Malis, an ancient Altenish fortress. As the crew narrowly escapes from the cave collapsing on them, Celestan also retreats from the chaos. All of the remaining Mana Stones are in enemy territory. The crew decides to return to Wendel…

Roget and crew arrive at Wendel as Pedda’s attack on the holy capital commences. An all-out defensive battle begins. The warp cannon on the magic fortress sinks the Peddan warship, and Wendel is saved. The crew must now head to Gusthall in Laurent…

The Nevarlan chief, Olbex, was waiting for the crew at Gusthall. Cornered after a fierce battle, Olbex kills himself by detonating a suicide bomb. The crew rescues Minerva, and recruits the wind spirit Jinn. Now only the spirit of the moon and the spirit of shadow remain. They head for Chartmoon Tower in Ferolia, land of the Beastmen, where they know the Mana Stone of the moon can be found. Luna is the last of the elemental spirits whose whereabouts are known…

At Chartmoon Tower, Luna, the spirit of the moon, joins the party. The time has come to attack Lowenburg, now a stronghold on Pedda’s front line. The enemy will most likely fight without mercy. Could this be the last battle…?

Roget and crew win the battle at Lowenburg. but the enemy uses the battle as a diversion to place another mirror of Esina in Wendel. Peddan King Inath orders his troops to retreat and utters ominously: “The real battle has yet to begin.” Inath’s words weigh heavily on the minds of Roget and crew even as the people rejoice in victory…

With the Peddan forces having pulled back, the only other remaining threat in the land are the Nevarlans. A battle ensues against the Nevarlan troops led by Flamekahn. Falcon’s feud with her father is settled, and an armistice is reached with Nevarl. The fragile bond between father and daughter is restored…

Esina’s mirrors shine menacingly in every country. Roget and crew decide they must go to Pedda in order to achieve true peace. But the Nightswan cannot handle the long-distance flight. The crew heads for the Celestial Peak to see if the guardian spirit would be willing to help them. Waiting for them in ambush is Celestan. The crew defeats him once again, and succeeds in meeting the winged defender. Roget and crew are now headed for Pedda, oblivious to what awaits them…

En route to Pedda, Roget is met by his fiancée, Elena, who awaits him above the sea. Elena cannot forgive Roget, who not only betrayer their country, but also drove her brother to his death. After a battle with the mighty Vuscavs, Elena senses her defeat, and crashes her ghost warship–and herself–into the magic fortress. Roget is stricken with grief as the crew finally arrives at Pedda…

Roget and crew fight against Pedda’s main forces at the royal castle. They finally surround and corner Inath. Just as it seems they could bring the king to surrender, Esina’s mirrors come to life all over the land. As the mirrors absorb Mana, every living thing in nature is altered. Inath calls for the giant warship, the Vel Vimana, and fires its cannons at the castle, with Roget and crew still inside. The royal castle falls into ruin. The Ve Vimana departs for Mirage Palace, where the real Esina’s mirror is supposed to be…

D’Kelli leads Roget and crew to the Jungle of Visions. By destroying the mirror shards, they arrive at Mirage Palace. There they find the real Esina’s mirror, as if it were waiting for them. With an eerie gleam, a man emerges from inside the mirror. He looks identical to Roget. And as he smiles, the eight spirits are pulled into the mirror…

The strange man is the Mirage Bishop, and Roget’s elder twin. The powers from Esina’s mirrors all over the land join as one, awakening the real mirror toits true power. Mana’s Sanctuary is dragged out by the mirror’s force; Mana from the Sanctuary rushes into Esina’s mirror. As “Psi” appears and glows int he sky, the world inside the mirror becomes clear. Esina was a mirror image of the real name–Anise. The mirror was of the great witch. And as unknown powers grow into a fierce maelstrom, Roget and the party are pulled into the mirror…

Roget and party have been sucked into a world inside the mirror. The dark world is separate from Mana’s realm of power. Surrounded by swarming enemies, the party’s fate seems sealed. But then the winged guardian opens a tear in the dark skies, whence the Sword of Mana flies down. Along with the word, the eight elemental spirits are also back. Equipped with the Mana Sword, Roget defeats the enemies one by one. But the bishop still smiles, and tells Roget of his plans to create a new world using the powers of Anise’s mirror. The bishop walks away as he suggests a change of venue for the showdown.

The trio awaits Roget and party. Baxilios wants the merciless world to atone for its past. Inath childishly talks about the fun he is having in building another kingdom. And the bishop, enchanted by the mirror, shares his dark dreams of a new cosmos. The battle with the mirages begins. Roget rips through the mirages with the power of the Mana Sword. Sensing defeat, Baxilios unleashes the power of the mirror, wishing the destruction of the world, just as the great witch once did. The mirror changes form as it devours the world. Inath is swallowed by the world that melts down around them. And by the great witch’s curse, Baxilios becomes a black goggess of doom. In order to stop the world from falling into ruin, the last battle must begin…

Roget and party finally come face to face with the black goddess of doom. In the midst of battle, Cecilia Baxilios and Yurchael meet in their minds. Cecilia says the Sword of Mana can break Anise’s mirror. Roget successfully destroys the mirror with the holy sword. Darkness overflows from the goddess. Roget and party cut through and clear the darkness with all their might…
And then it is all over.
What is left is a whirlpool of realms. Beyond it, they learn that there are countless other realms where Mana and Anise are fighting.
Roget and the Nightswan crew vow to continue battling Anise as they depart for the realms beyond…