Final Fantasy II begins with Firion, Maria, Guy and Leon being attacked by imperial soldiers and left for dead. Firion, Maria, and Guy are rescued by Princess Hilda of Fynn, who has established a rebel base in the nearby town of Altair after the Emperor's capture of Fynn. Hilda denies a request by Firion that he, Maria and Guy join the rebel army on the grounds that they are too young and inexperienced. Eager to prove their value to the resistance movement, the three set off for the besieged Fynn, where the four find an ailing Prince Scott of Kashuan, Princess Hilda's fiancé, in the basement of the rebel-friendly local pub. Scott dies of his wounds from the battle of Fynn against the Emperor, but not before giving the party his ring, which reveals the world map. He also informs them that Borghen betrayed the rebellion and became a General in the Imperial army. He tells the party to tell Hilda that he loves her, but retracts the request, and dies shortly afterwards. The three adventurers return to Altair and present Hilda the ring, who after an emotional reminiscence of Scott, allows them to join the rebel movement.
Having proved their worth, the party is charged with journeying to the mountainous northern parts of the world to find Mythril that the rebels need to make weapons that can measure up to that of the Empire's. Before leaving, the party is joined by the White Mage Minwu, who healed the party at the beginning of the game. The party sail across the ocean to the eastern continent and make it north to the mountain village of Salamand, which is under siege by the Empire and are forced to mine Mythril for the Imperial army. There they meet Josef, the hero of the town, who informs them that the men of the village are being forced to mine Mythril in the Semmit Falls. Josef, however, can do nothing, as his daughter, Nelly, is being held captive.
The party enters the mine and saves the captives, including Nelly and Paul, who is supposedly the world's best thief. The party defeats an Imperial soldier and returns to Altair with the mithril. The party is then told to go to Bafsk, which is under General Borghen's command and is easier to infiltrate. However, the party is too late to stop the Dreadnought from being completed. A plan is formed to use the Sunfire from Kasuhan Keep, but to enter, either the Goddess Bell or the voice of a Kashuan is needed to open the keep. Josef helps the party enter the snow caves with a snowcraft, and the party retrieves the bell. On the way out, Borghen attacks the party, and although he is defeated, he sends a boulder after the party. Josef holds back the boulder to allow the party to escape but is crushed to death.
The party reaches Kashuan Keep, where they find Gordon has already entered. Although they retrieve Egil's Torch and use it to capture the Sunfire, the Airship - with Cid and Hilda on board - is captured by the Dreadnought's crane arm. The party enters the airship and saves Hilda, before throwing the Sunfire into the engine. Immediately after doing so, the Dark Knight appears, and Maria recognises his voice before she escapes.
The King of Fynn, now close to death, summons Gordon, Minwu and Firion's group into his bedroom and gives them assignments. Gordon is given command of the rebel army, Minwu is told to find the Ultima Tome, and Firion's group is given the task of finding the seemingly extinct dragoons of Deist. The king then dies of his wounds. Firion's group realizes that no captain will take them to Deist save one- Leila. Leila, however, turns out to be a pirate, and orders her crew to attack Firion's party. The party fights them off, and although Leila expects that Firion will kill her, he instead asks for her help in taking them to Deist, a request with which she complies. In Deist, the party finds only a mother with her son, learning that the all but one of the Dragoons and all but one of the Wyverns are dead, partly as a result of Imperial poison. The party obtains a pendant to speak with the last Wyvern, who tells the party to take its egg to a pool deep in the cave before it dies. The party plants the egg in the cave, and fights off some monsters that come after it.
The party returns to Altair, where they learn that Hilda has been acting oddly, eating mice and acting seductively. She summons Firion to her room and tries to seduce him, revealing her true form as the Lamia Queen. The party defeats the Lamia Queen, and learns that they had rescued a decoy on the Dreadnought; the real Princess is in the Arena; Gordon goes to save her while leaving Leila to run the rebellion. The party defeats a Behemoth to win the Princess, but the Emperor tricks them and has the Dark Knight and his soldiers capture and detain them. Paul, however, breaks them out, and the party saves the real Princess.
Upon their return, the party learns that Hilda and Gordon are launching an attack on Fynn, and infiltrate the castle to kill the commander of the enemy forces. Hilda then tells the party that Minwu has not been heard from for some time, and tells them to search for him. The party acquires a Crystal Rod to enter the tower after acquiring the White and Black Mask, but Leviathan swallows their ship and separates them from Leila. They meet Ricard (his name is based on the Game Boy Advance translation, and varies significantly with the translation), the last surviving Dragoon, who had set out to find the Ultima Tome, and they join forces. After gaining another ship, they sail to the Magicians' Tower. At the top, Minwu explains that he was waiting for the party and then casts a powerful spell to shatter the Ultima Tome's seal, at the cost of his own life.
The party returns to Fynn and sees that many towns have been destroyed by the Emperor's Cyclone. The party calls upon the newly born last Wyvern to take them to a castle inside the Cyclone, where they confront and kill the Emperor. Everyone celebrates the Empire's defeat, but a mortally wounded soldier arrives and reveals that the Dark Knight has taken the throne and plans to destroy the Rebels with the Imperial army. He then makes a more shocking revelation- that the Dark Knight is Leon, Maria's long-lost brother. The party realises that they will have to infiltrate the castle of Palamecia from the air after talking with Paul and receive the airship from a dying Cid, who was mortally wounded by the Cyclone.
The party enters the castle and confronts Leon. Then, the Emperor returns in a new demonic form and reveals that he does not seek to regain the Empire but to destroy the entire world. As he summons magical fire against the party, the Wyvern arrives and takes the party to safety as Ricard holds off the Emperor and dies. Princess Hilda is shocked to see Leon on their side, but Maria convinces her to trust him, and Leon agrees to help his friends and sister once again.
The party then enters the Jade Passage, an underground cavern near a lake, and find a portal to Pandemonium. The party fights its way through the fortress, and reaches the Emperor at the top, defeating him for the second time. The party then receives congratulations for their efforts and learns of Hilda and Gordon's plan to unite Fynn and Kashuan, which may indicate that they plan to marry. Paul is upset that he will no longer have the Empire to steal from and suggests that he will steal from the former rebels. Leila invites Firion to become a pirate, but Maria objects and Leila suggests that Firion will have to deal with her in the future. Maria hopes that they will live together as they once did, but Leon says that they cannot live together again- some translations have him indicating that they know too much about each other, which may refer to his lust for power. Maria begs Firion to stop him, but Firion believes that Leon must follow his own path, but tells him that they will be waiting for him, as though he hopes that Leon will return someday.
The Soul of Rebirth scenario (only on the Game Boy Advance version) has all those who have died reunited.
Minwu awakens in a strange cave, similar to that of the Jade Passage. He then encounters Scott, Gordon's brother who died earlier in the game and helps him defeat some Black Knights and a revived Zombie Borghen. They then carry on through the passage, where they encounter Josef and later Ricard, after which they defeat a Roundworm that had followed him. They are unsure of the reason why they have been reunited. Soon, they discover a portal, which leads them to Machanon a town inhabited by all who have died including Tobul the smith as well as Cid, who tells them that the town has been terrorised by monsters.
A portal they find leads them to a tower very much like the Tower of Mysidia. There they receive spiritual power and they defeat Ultima Weapon to obtain this world's version of the Ultima Tome. The other portal leads them to what they believe to be Pandaemonium. After fighting their way up to the top, they encounter an entity which says he is the Emperor's light side, as opposed to the dark side causing havoc on Earth.
The light Emperor explains that the passage was Raqia, not Jade and that the palace is Arubboth (Heaven)and that they have been brought back to be asked for forgiveness, which they decline, thinking he is mocking them after visions of their friends on Earth appear, showing them Firion, Maria, Guy and Leon fighting the Emperor on Earth. They defeat the light side and observe their friends on Earth returning to normal after the Emperor's defeat. Minwu explains that they do not need their help as they have grown strong.
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