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Breath of Fire II begins with an intro sequence of Ryu (the default name of the game's protagonist) at a young age (presumably between 7–10 years of age) living in the quiet village of Gate with his father Ganer and sister Yua. One day Yua goes to see the Dragon Guardian which sleeps behind their village and Ryu is sent by his father to fetch her for her nap. After Ryu meets with her, his father shows up and they head back to the village leaving Ryu alone for a short period. When Ryu returns to his village, he cannot find any sign of his father or sister and mysteriously, none of the villagers know who he is or seem to remember him. He is taken in by the new priest of the St. Eva church, father Hulk, who replaced Ganer. He then meets and befriends an orphan named Bow(Boche in the Japanese version). Ryu and Bow decide to steal anything of value from the church and leave. It begins to rain as they leave the village of Gate and they take shelter in a cave. Once inside the cave they encounter a colossal demon known as Barubary. The demon alludes to Ryu being the "destined child" and attacks him, nearly killing the child.
Ryu awakens in present day as a fully grown adult with his friend Bow, living in the town of "Home Town". They have joined the Hunters guild, which is a small organization of mercenaries and hirelings. Their first task is to retrieve a pet pig, which they do so. In the process they save an old man, Niro, in a dilapidated house from a horde of huge savage roaches, however robbing him of his meal. Their jobs with the Hunters Guild continues and Bow is framed and implicated of the crime of stealing from the richest man in Home Town. To protect Bow from being falsely imprisoned, he goes into hiding with Niro, working to improve the collapsing house while Ryu searches for the real thief who framed Bow.
Ryu's quest takes him all across the continent in search of the real thief, where he makes a number of allies and faces off against a number of enemies. Among the allies he makes is a very large, muscular, member of the Shell Clan named Rand. He helps Ryu save a Woren fighter named Katt(Rinpoo in the Japanese version) from a crooked Arena Battle that Ryu was forced to take part in. A Windian princess and magician named Nina. A acrobat/con-artist of the Highlander tribe called Sten and a foppish Creeping Clan prince known as Jean(Tapeta in the Japanese version). Ryu helps all of them in one way or another and they repay him by joining him in the search to find the real thief and clear Bow's name. During one incedent in the town of Capitan where the townsfolk were being attacked by a swarm of large insects; Ryu and the party are assisted by a disciple of the church of St. Eva named Ray who wields powerful holy magics and acts very honorable and kind.Ryu and company eventually track down and capture the real criminal who implicated bow, Patty the Phantom Thief, in Jean's kingdom of Semafort. They bring Patty back to Home Town to face punishment at the hands of Trout, the person she stole from. Patty reveals that Trout hired her to steal the item in the first place and that Trout is the real criminal. Trout confesess to this and transforms into a hideous demon, professing he is acting in the name of his god, and attacks the party. After Trout is defeated and Bow's name is cleared, the party convenes at the Hunters Guild to recap the situation as a report comes in of a massive Demon at Ryu's hometown of Gate and the forest surrounding the town mysteriously beginning to die. The party realizes that throughout their quest they have encountered several demons disguised as humans who have been committing atrocious acts in the name of their "God" and that it could somehow be linked to the demon appearing in gate and the forest dying.
Ryu's party goes out in search of the "Grass Man" a being said to be able to communicate with plants and trees to see if he can shed light on why the forest aroudn gate died so suddenly. The party locates the "Grass Man", a member of the Grass Clan called Spar(Aspara Gus in the Japanese version), and save him from being devoured by another demon disguised as a human. Spar decides to join them and assist in their quest to save Gate and get to the bottom of why so many demons have been appearing in the world. He takes them to the "Great Wise Tree" called Gandaroof, who should be able to communicate with the Trees dying in gate. The Great Wise Tree's memory is being destroyed by an unknown source however and the party must go into his mind to eliminate the source of his memory problems. After much time and effort spent finding a method to enter Gandaroof's mind the party eventually does so and discoveres a demon named Aruhamel inside him which is devouring his memories because they are inconvenient to his god. The demon also confesses that it was he who devoured the memories of the people in Ryu's hometown years ago which is why they did not remember him. The party defeats the Aruhamel and Gandaroof is able to give them information to assist them in their quest.
Ryu and company eventually come to Evrai. The main city of the St. Eva religion which has been spreading throughout the world and has been one of the main backdrops and factors in the game. On the surface the city seems to be full of happy and prosperous St. Eva worshipers, however when the party attempts to leave the city they find some mysterious force that will not allow them to leave. The inhabitants of the city at that point change into a behavior that is very much like zombies, mindless and mummbling they are cold and cannot see anything, yet still praising St. Eva. The party eventually finds one person a woman named Claris, who is not like the others, yet is a member of a resistance group fighting against St. Eva. She helps them escape Evrai and sends them to meet with the leader of the resistance, a strong Woren named Tiga. Tiga tells Ryu and his team that St. Eva is a wicked religion that does many evil things in the shadows and asks them to help his group destroy the grand church and defeat St. Eva. Ryu and company agree and after much preparation, they go to Evrai and the grand church to enact their plan. As the party is entering the church it is said that the name of the deity of the St. Eva religion is Saint Evans.
As they enter the grand church, they see the high priest and founder of St. Eva, Habaruku, giving a sermon. Habaruku begins by speaking about those who don't believe in St. Evans. He even goes as far to say that there is a nonbeliever in the room as he speaks. He then reveals Claris trapped in a magical bubble. People at the sermon begin to order her to be killed, however Habaruku attempts to turn her into a believer of St. Eva. He reads her mind and reveals that she knows all about the resistance and that she is in love with Tiga. This inspires Tiga to blow his cover and attack Habaruku to save Claris. Habaruku easily evades all of Tiga's attacks and defeats him in a single blow, he then murders both Claris and Tiga together and ends the sermon. Ryu and the party head after Habaruku, however they encounter Ray and Habaruku tells him to take care of Ryu and his friends. Ray transforms into a dragon and attacks the party. During the battle when Ray attacks Ryu, it unlocks a new ability within him allowing Ryu to transform into his most powerful dragon form the "Grand/Gold Dragon" which Ryu uses to defeat Ray in a single attack. After his defeat Ray tells the party that he will add his power to Ryu's to aid them. After Ray dies, Habaruku says that Ray was worthless and flees into the deeper sections of the Grand Church.
Ryu and company pursue Habaruku into the depths of the grand church of St. Eva and eventually come to a large machine with Ryu's father, Ganer, hooked into it. Ganer begs the party to kill him as his life force is being drained and sent to a sleeping demon that will awaken soon. The player has two choices at this point, either kill Ganer and thus destroying the machine, or attacking the machine itself while avoiding Ganer. If the player chooses not to harm Ganer, he survives and this can lead to one of the "good" endings. If the player kills Ganer he dies after the battle and a relatively "good" ending can still be attained, but the player will not be able to take advantage of some plot aspects of keeping him alive. Regardless, after the machine is destroyed, the grand church crumbles and the party heads to Gate on the advice of the Great Wise Tree. Once they arrive in Gate father Hulk and Patty are there talking about the current state of the Dragon Guardian. Suddenly, the dragon speaks out in a voice asking everyone to leave immediately in case the Demon which is sealed up inside the gate it is guarding, is released.Father Hulk reveals that he is truly Habaruku. Habaruku tells everyone the story of how the Dragon Clan sealed up the Demon God in Gate. Habaruku prepares to kill Patty in an attempt to sacrifice a member of the Dragon Clan to open the sealed gate, but the Dragon Guardian saves her. The party then fights and defeats Habaruku. The player is given a choice at this point whether to enter the Gate and defeat the Demon God or merely wait and hope that it never escapes. If the player chooses the "Wait" option, it leads to the "worst" ending in the game. If the player chooses "defeat" then the story goes on with Ryu and his party entering the sealed underground dungeon to face the Demon God. The party eventually comes to a city on a tower in a massive underground cavern. The city is Dologany, the city of the Dragon Clan.
Through a flashback sequence, it is revealed that Ryu's mother's name was Valerie and that after marrying Ganer and birthing both him and Yua, she gave her life to seal up the Demon God and become Gate's Dragon Guardian. The party descends further into the massive underground cavern and comes to a Dragon Clan shrine where the greatest power of the Dragon Clan is kept. Ryu must choose one of his companions to sacrifice so that he can gain the ultimate dragon power. Ryu refuses to sacrifice any of his friends through an emotional struggle within himself, however this was the correct choice and Ryu is bestowed the "Anfini" ability. They journey deeper and eventually come into contact with Barubary, the same demon that nearly killed Ryu when he was a child. It is probably the most difficult boss battle in the entire game, but the party defeats Barubary and proceeds to the Demon God himself.
Ryu and company come upon the god of the St. Eva religion, Evan, an aged man in a flowing robe who eeriely hovers above the ground. Evan refers to Ryu as "Nikanoru" which he states, when questioned, is a word used to refer to dead beings. He then encases Ryu and his friends in crystalline, from which Ryu breaks free. This annoys Deathevan so he paralyzes Ryu with a spell then tells Ryu that he cannot hope to match the power of "God", he then begins to shatter each of Ryu's friends who are encased in crystalline, killing them. He states that lives crumble so easily on God's hands and that they are nothing more than insects at his feet. After he has killed all of Ryu's friends, he disappears and leaves Ryu paralyzed.
Ryu, enraged, breaks free of the paralysis and charges after Evan, running headlong through a barrage of fire and explosions which Evan summons to block his path. He rushes at Evan and slashes him with his sword. This sends Evan into a fury and he reveals his true demonic form, Deathevan. The battle begins and the only way to defeat Deathevan is for Ryu to use his "Anfini" power. Ryu activates it and memories of all his friends and the people who are counting on him flood into his mind. All of Ryu's friends are brought back to life by the power of Anfini and rejoin him to fight against Deathevan.
After a difficult battle Ryu and his comrades defeat Deathevan. The Demon God slowly vanishes into the darkness saying that he will sleep and dream of death until it comes time for him once again to emerge, leading the heroes to believe he is not truly defeated. Once the party emerges from the depths of the dungeon one of two posssible endings can occur depending on choices made in the game.
The "Sad" ending occurs if the player was not able to make the customizable town, Township, fly. As the party heads out of the final dungeon Ryu recall's Deathevan's words about returning and what the Elder Dragon Clansman told him about fullfilling his destiny. The party leaves gate and they notice Ryu is missing, they look back to see Ryu is the new Dragon Guardian protecting the seal so that Deathevan cannot return. The party attempts to talk to him and wake him up, but they cannot.
The "Best" ending occurs if the player was able to make Township fly by not killing Ganer and recruiting Eichichi into your town. This is nearly identical to the "Sad" except that when Ryu is about to transform into a Dragon to guard the Seal. The flying Township shows up with Ganer piloting it and it drops down onto the mountain behind gate, completely sealing off the underground. Ganer tells his son to go out into the world to spread true joy and happiness so Deathevan will no longer be able to feed on the fears of the people. Ryu then rejoins his friends for good.