As described in the game's introduction, the story is set twenty years after the events of Shining Force I. Ken, Lowe, and Luke (mistranslated as "Lug") have helped rebuild Gardiana after the destruction caused by Runefaust, and now serve Anri, Gardiana's queen.
The story begins with the arrival of a trio from Cypress, headed by Woldol, Cypress' ambassador. After Woldol uses a bolt spell to dispatch some guards, he and his cohorts make vague threats. They then offer Anri a gift, which, when opened, engulfs her in a black fog. Apparently Anri has been put under a sleep spell that only King Edmond of Cypress can lift.
Gardiana sends it's best soldiers (including Luke) to Cypress to kill Edmond (regicide = diplomacy), but a month after the army set sail, it's disappeared. It seems as if Gardiana will have to knuckle under to Cypress... Then Ruce appears with a force (that, save for Nick, consists of relatives of the original Shining Force), and explains that he and his friends, led by Nick, plan to defeat Cypress. Lowe will accompany the group as an advisor, and Ken will stay behind to handle things in Gardiana.
The group sets sail for Cypress... but soon runs into trouble. They're attacked by a Dark Mage, who, after being defeated, sets fire to the ship. Forced to abandon ship (and all of their supplies), the group swims to a nearby island. When everyone washes ashore on Miniyom, they encounter some Cypress soldiers harassing the locals. Naturally, the Force vanquishes the oppressors, and one of the locals joins the Force in support against Cypress. The Force then proceeds to Miniyom Bastion from which, with the help of Claude (who is part of the Cypress Resistance), they procure another ship.
With Claude leading the way, the Force sails to Asreet Island, the base of operations for the Cypress Resistance. By the time the Force arrives, Cypress is busy trying to smoke out the Resistance fighters. After beating back Cypress, Stock and Mayfair, also of the Resistance, join the Force. The Force continues on to Bazoo's Tower; since he's Woldol's right-hand man, he can probably be pumped for information. After defeating Bazoo, Yeesha joins the Force, and it is revealed that Nick is actually the Prince of Cypress, which casts some suspicion on him.
The Force continues sailing to Cypress, but the ship is stopped and searched by customs. After some Force members get by the inspection with bogus stories, King Edmond shows up, recognizes Nick, and demands that he be arrested. After a brief scuffle, Gyan, one of Nick's allies, shows up and explains the situation to the Force. Apparently Nick's father, the King of Cypress, was killed by Edmond or Woldol, and after Cypress was taken over by that duo Nick travelled to Gardiana to get help. Gyan joins the Force and sets them on a course toward Cypress' palace.
After making their way through the pampas, and the Death Tunnel (where you meet up with Kashing, who was in the army sent to Cypress in the beginning of the game), the Force arrives outside Gundoll fort. Dantom and Frabell are there to greet them. Though she does not face the Force directly, Frabell sends her soldiers. After she fails, the fight carries on into Gundoll fort, where the Force faces off against Dantom. Dantom doesn't really want to fight, but he's bound by honor to do battle for Cypress. When he is defeated, he warns the Force about Woldol, who he says worships an evil spirit called Iom.
Now that the Force has made it through Gundoll fort, they can proceed into Cypress. Edmond, though, meets them on the battlefield. Once beaten, Edmond calls Nick a traitor, believing Nick killed him to claim the throne. Once the Force has made it's way to the castle gates, they'll have to get by Geppel. Inside, Bazoo and Frabell will hold off the Force long enough for Woldol to summon Evil Monster. They'll then do battle with Woldol and Evil Monster.
With the monster beaten, Woldol starts to take off, but is stopped by Luke. Luke, brandishing the Sword of Hajya, explains that it can injure Iom, and that Woldol wanted to take over Cypress so he could obtain and destroy the sword. Woldol, who simply must have the sword, transforms himself into a giant scorpion thing, and attacks. During the battle, Woldol spits venom on Nicks right arm.
Once Woldol is finally defeated, Luke and his son, Ruce, have a cheerful reunion. While that is going on, Nick passes out as his arm, covered in vemon, turns to stone. Iom then makes his presence known, telling Nick that, in order for him to restore his arm, he'll have to face Iom sometime in the future.
With the villains defeated, the spell on Queen Anri is lifted. With Edmond vanquished, Nick now sits on Cypress' throne. Peace between the two countries is restored. Cypress makes plans to explore the interior of the continent, in search of Iom and his servants.
The story begins with Warderer, King of Iom, sacrificing the King Emild to Iom. After appeasing the dark god with royal blood, Warderer discusses his plans with his lackeys, Barbara, Solo, and Hindel. They'll be preparing for the Cypress army, which is marching toward Iom, but to secure victory, they'll need to sneak the Sword of Hajya out of Cypress. The latter task is assigned to Gordon.
As Prince Nick of Cypress is about to set off with the Cypress army in tow, Dawn and Natasha bring an injured boy, Deanna, into the castle. With Nick and the Cypress army gone, a small force consisting of Deanna, Dawn, Natasha, Luke, Eric, and Jaha is left to watch the castle, which has been left in the charge of Mayfair.
While some of the group is slacking off on their guard duty, the castle is attacked by Iom soldiers. During the battle, Graham sneaks into the castle and makes off with the Sword of Hajya. The Force follows him to the Thames village, where they meet Slade. Apparently Iom soldiers have taken the people of Thames hostage in order to get Graham to steal the Sword of Hajya for them. Slade, believing the Force can save the villagers, joins up and points them toward the Albert Cliffs, where the villagers are being kept, and where Graham intends to exchange the sword for the villagers' freedom.
At the top of the cliffs, Graham gives a Dark Mage the Sword of Hajya, and gets attascked by Iom soldiers for his efforts. Iom intended to kill the villagers all along, but the Force shows up just in time to stop them. Once Dark Mage is defeated, he gives the Sword of Hajya to a Gargoyle, to fly it to Gordon. As the Gargoyle takes off, Graham shoots it out of the sky.
The Force makes their way down the cliffs, and begins searching the area where the Gargoyle went down. When that turns up no results, Eric suggests that maybe someone found the sword, and took it into Emild castle. A group of Iom soldiers, posing as Emild's soldiers, attacks the Force. Once they're beaten, Chester, one of Emild's subjects, tells you that the King has possession of the sword. During their meeting with the King, it is revealed that Warderer sacrificed King Emild to Iom, and that Gordon has been posing as the King. Gordon causes the castle to partially collapse, and flees with the sword. The Force shortly catches up to him, and regains the Sword of Hajya after defeating him.
With the sword back in Cypress' possession, the group prepares to return to Cypress, but is halted by a strange voice. The vioce tells them that Prince Nick and the Cypress army were defeated and taken hostage, and that to save him, the Force will have to go to Portobello, and get a ship to sail to Iom.
In Portobello, the Force learns that Nick is being held at Algam fort, a heavily defended Iom position. The Force begins boarding a ship to sail to Algam, but is interrupted as Randolf and Sarah, members of the Cypress army, show up and warn that the ship is a trap. Their warning comes too late, and half of the Force is taken away by the ship, while the other half is left in Portobello.
After a few failed attempts to regain control of the ship, Deranna's half of the Force is attacked. After the battle, Claude shows up. He tells you that the ship is sailing toward the port of Demis, and from there the Force can make it's way to Algam. Once the ship has landed, Deanna's Force begins the journey to Algam fort over some unstable volcanic ground. Iom soldiers are waiting for the Force, and a battle ensues, after which the ground opens up and swollows the Force.
Meanwhile, Natasha's Force is proceeding towards Algam on foot. After dispatching some Iom soldiers, the Force encounters a village who's townspeople built Algam fort. Rphde, one of the villagers, mentions a weakness in the fort. After joining the Force, he informs you that, despite the fort's great ground defenses, it is vunerable to attack from above. And so the Force uses the nearby cliffs to attack the fort from the top.
While that is going on, Deanna's Force is making their way through some underground caves. After a battle, they reach a dead end. With the Iom army following behind them, the Force is facing certain destruction. But someone lowers a rope down to the Force, and helps them escape the caves. Once out of the caves, Deanna's Force meets up with Natasha's Force, and they turn their attention to the castle on the Algam fields.
Within the castle, Barbara and Solo are bickering with each other, to the annoyance of Hindel and Warderer. Warderer seems to suspect a traitor within the Iom ranks, but before he can put a name to his suspicions, the Force arrives. Solo is left to hold up the Force while Barbara, Hindel, and Warderer leave for the shrine to Iom, planning to sacrifice Nick there.
Once Solo is defeated, the Force heads for the shrine, pursuing Warderer. Iom soldiers slow their progress, but they eventually arrive at the shrine. Warderer and Hindel take Nick into the shrine while Barbara is left to slow the Force. After defeating Barbara, the Iom army shows up, but is held back by Gardiana. While the two armies clash, the Force enters the shrine, wherein they encounter Woldol, who's soul has apparently been restless without mayhem.
After getting by Woldol, the Force enters the main part of the shrine. Warderer has discovered the traitor - Hindel - and is kicking him all over the shrine. Still, the plan is to sacrifice Nick before dealing with Hindel, so the Force jumps into the fray. After the battle, Hindel unbinds Nick (who's arm is restored, now that Warderer is defeated), and tells the Force to use the Sword of Hajya to finish Iom. Nick then reveals that Deanna is Hindel's brother. Their celebration is cut short when Warderer throws Hindel into the lava, then jumps in the lava himself. Shortly thereafter, Iom himself comes up out of the lava. With the Sword of Hajya, the Force ends the reign of Iom.
In the aftermath of the battle, the shrine begins crumbling without Iom's power to hold it together. Deanna refuses to leave Hindel behind, and stays while the building collapses around him. Natasha and his friends manage to talk some sense into him, though, and he does eventually leave.
Back in Cypress, a while later, Deanna plans to leave Cypress to find his own adventures. Nick and Gyan try to convince him to stay, but it's futile. As he reaches the castle gates, a tearful Natasha decides to go with him.
So there you have it. Good triumphs over evil, the hero gets the girl, and the two of them ride off into the sunset. Happy ending.
... Well, I don't want to ruin everything. Play 'em yourself :þ