Some time prior to game's start, Oalston starts to study black magic, an ancient art which usually corrupts people's souls, but has no negative effect on him. After some time, Oalston falls ill and since then he stays in his home at Village of Trei being looked after by Dr. Cunnings. Later, the dragoons Vahn and Hans arrive with the Ancient Scale which he hands over to the doctor in order to prepare a medicine needed to heal Oalston's illness. Suddenly, a guard arrives saying that Maria went into the town's underground caves where monsters reside. Oalston quickly gets up from the bed and goes with Vahn and Hans to the caves in search of Maria, much to doctor's warning. They found Maria in the Caves attacked by a monster, but Oalston defeats it with his magic. After they return to his house, Dr. Cunnings injects the cure into Oalston. After the doctor asks why Vahn helped Oalston return to his health, the dragoon explains the situation: a man called Darius who obtained power over black magic, how it corrupts his mind, and Lord Adder's request to dispose him. Oalston suggest performing a "purification", a process which removes black magic from a person, but requires a skilled white mage to do so. Hans suggest requesting a permition to use the Eternal Blue in order to speed up the process of finding a white mage to which both agree. At Branch Castle, Lord Adder informs them that Vicks is currently in Lenadia with the ship and it can't be used. While discussing various possibilities, Oalston mentions a town called Mystic Mysidia where mages live, and Lord Adder asks them to go there also requesting Hans to stay at the Castle if Darius were to pull something and Vahn and Oalston take Wedge from the Water Shrine with them. After getting Wedge, the three go through Trei Catacombs and Vahn and Wedge pass across Ivalice Checkpoint in their cilivian attire to not raise suspicion among Ivalician soldiers.
In Mystic Mysidia, Oalston, Vahn, and Wedge notice an argument between the town's Elder and the Ivalician generals. When the general Deckar and Eva are angry about Vera's way of interrogation, they attack her, but the party protects her. After the battle, Deckar and Eva leaves, and the Elder explains them the situation: a man clad in black armor wielding magic attacked the Citadel earlier that day and Vahn concludes that it must be Darius and they came to the town to seek a white mage who could remove the black magic from the corrupted dragoon. After discussing where the party could find Darius, Vahn theorizes that he may be after Crystals, and Elina notices the disappearance of Mysidian Flame, a symbol of Fire Crystal's well-being. The party decides to investigate the matter by going to Mount Gulgur where the Crystal resides. After passing through Mount Mysidia, Elina informs the party they will go through the abandoned town of Niflheim which lies beneath the volcano. Arriving at the Crystal Chamber in Mount Gulgur, the party meets Malacore, who reveals to them that he was constructed by King Branch during the Crystal War to be used as a last resort to control the Crystals' elements. He further states that he used Darius's weak spirit to influence him in gathering Crystal power so his seal connected with the Crystal of Water woulf shatter releasing him. He then states that he wishes to rule the world and Malacore engages the party, but looses, however he still stands and casts Firaga on the Crystal of Fire, releasing Rubicant, the Fiend of Fire, in the process. Rubicant is outraged by Malacore's actions and noticing Vahn and his group asks them if they are responsible for the attack on the Crystal. Malacore says that humans are the reason for the world's downfall and asks the Fiend of Fire to lend his power to his "cause". Rubicant agrees and fights Vahn and his party, defeating them with ease. Rubicant then lends his power to Malacore and is seemingly absorbed into him. Vahn decides to return to Branch to report to Lord Adder. At the exit of Mount Gulgur the party meets the Elder of Mysidia who informs them that the Mysidian Flame has extinguished itself and Vahn asks him for the quickest route back to Branch. The Elder informs them of Gozmodan's Grotto in the Arena that the owner will allow them to use and invites the party to rest for a night at Mysidia.
The next day, Vahn and his party arrives at the Arena and asks its owner for passage into Gozmodan's Grotto, which he is granted when the owner notices him to be a "military type", hence able to survive in the passage. At the exit of Gozmodan's Grotto, the party encounters the Esper Syldra, whom they defeat in battle and Vera acquires her services. Back in Branch Castle, Vahn relays to Lard Adder everything he has learned at witnessed after departing for a white mage. Lord Adder suggests to capture Malacore i order to study him and learn of what drove King Branch into starting the Crystal War in the first place. When Vera starts asking the Lord what he will do with Malacore after everything is done, the man admits he hasn't thought it that far, and Vera criticises him for that. When Lord added starts to speak about a prophecy, Vahn interrupts asking him about it. Lord Adder reveals it is an ancient prophecy which speaks about the end of the world "as they know it". If the elemental balance would be disturbed the world would be shrouded in darkness, but the real consequences are unknown. Lord Adder then advices Vahn to search for Hans in the east who has gone after Braak. Vera reveals that he answers to Lord Zeul, but she is unable to think of a reason why he would send the general to Branch. With the Serpent Road mysteriously out of service, Lord Adder suggests them reaching Eternal Blue via Old Branch under the castle. In the Old Branch, the party discovers the spirit of King Branch who orders them to leave the place. As they do not show any intent on doing so, the spirit forces them to battle but looses. As the King is to fade away, he laments on his horrible acts while he was alive and says his goodbye to his son "wherever he is", shocking Vahn with this latter bit of information. The group then boards the Eternal Blue at the port in the east and sets sail. As Vahn and Vera wonder about Malacore's next course of action, the ship's crew suddenly transforms into Archareons and attack the group, with Gylfi as the lead. When Gylfi looses, he summons Hans to finish off the party, much to Vahn's shock. As the battle drags, Gylfi grows impatient and dismisses Hans who bids farewell to Vahn. The Archareon leader then calls forth Meteo and destroys the vessel, scaterring the party.
In the Kohlingen Cave, Vahn comes across Vera and Oalston fighting a chimera. After the successful battle, Vahn and his party reunites with Vera and Oalston who say that they washed up on the west coast. Vera informs Vahn that monsters try to converge around the Wind Crystal with little success and due to that many different monsters end up trapped on the Great Plain around Daguero. Vera and Oalston then inform the party of a shrine there were staying while waiting for a word from him and the two go there, saying that they will be waiting for them there. Vahn's party arrives at the Rift Shrine where they meet Ramuh who tells him to seek help in Lenadia to aid him in his quest of vanquishing Malacore, but warns the dragoon about someone who does not want him to interrupt what Malacore is doing: the Archareons, rulers of the Esper World. Ramuh says that Archareons believe that Vahn pursuing Malacore will bring about the Blackmoon Prophecy. The Esper hints at Vahn's lineage and binds himself to Vera. After arriving at Daguero by defeating Evil Wall in Rudra Cavern, Vahn and his party visit the town Elder who upon the dragoon's asking says that the town has no way to cross the mountains to reach the capital, but states that he has seen a map from the capital and suggests asking him about help. At the inn-pub the party comes across Cid, a head scientist, whom they ask about a way to the capital. The man reveals that there is a Serpent Road to the north in his laboratory, but the monster there is too strong for him. Cid then accompanies the party to the laboratory located on the Plain. There he explains that the monster that is at the top of the lab protects a cure for people who administer the Serpent Road and without it they won't be able to continue their journey. Midway through the tower the group encounters Magus Sisters who protect the tower from intruders for their master and force Vahn's party to battle but loose. Atop the laboratory, the party defeats Biblos that took residence in the place and defeating him earns the group Silvera Cure. Together with Cid, the party travels to a Chocobo Forest in Kohlingen's vicinity and with its help the group goes to an island where Silvera is located. Arriving at the town, a werewolf spots them and quickly hides in the local inn. When he knocks on the inn door no one responds, but after mentioning a cure for the town the door is unlocked and the party enters. Inside they notice a plethora of various monsters, with a werewolf one introducing himself as Arvis, the town Elder. Upon his request, Vahn hands him over the cure with the Elder promising to repay him provided the cure will help him and invites the dragoon to stay a night at the inn. By the morning the town is cured and when Vahn asks the Elder the keys for the town's Serpent Road he says that their keeper went to Kohlingen. The Elder says that the password that the keybearer will ask is "courage". From Kohlingen's Elder the group learns that the traveler from Silvera haven't stayed long and went to the Auction House. From a woman at the Auction House, the party learns the the traveler have learned some kind of pet and went to the west for some hiking. Atop Mount Matoya the group comes across the keymaster who is attacked by his pet Garuda, but they save him in time. Telling the password, the man grants them the key to the Serpent Road and wishes them luck.
At the South Shore Checkpoint one of the guards warns his colleague about the ghost haunting the building. The other guard refuses to listen to him and enters, the former one afraid that he will not be able to return home if his comrade will not return. The group then saves the other guard from the ghosts and the man opens up the gate to the east. As the group is about to leave the Checkpoint, Archareons once again ambush Vahn and his party, but they prevail and continue on their journey. On their way to Lenadia Castle, the party is stopped at one of the bridges leading to it and is asked to wait at Cornelia. In the port town they come across Siegfried, a world class swordsman. Initially he loaths the dragoon and attempts to get rid of him, but after the two share their stories, Siegfried offers to join Vahn on his journey, hoping that in his travels he will find Excalibur, the sword he is looking for. He then challenges him to a one-on-one duel as a form of test and Vahn bests him, resulting in the swordsman joining his group. The group then decides to spend a night at Cornelia, waiting for the blockade to lift off. Vera is thinking about Ivalice, when Ami unexpectedly joins her. Vera reveals to her that she must have a sleeping problem, but also a lot on her mind, especially since rejoining Vaan, and Ami takes it for a forming deep bond between the two. Vera denies it and asks Ami about her carefree behavior that somewhat contradicts her age, all while briefly being spied by Nobumasa. Ami says that behavior does not bother her and she can be serious, and she offers Vera to demonstrate it. Vera refuses and advises them to go get some rest or Vahn will have problems waking them up and the two retire to the inn. The next day the group arrives at Lenadia Castle where King Gorn informs them that the reason why the bridge was out yesterday was because of a diplomatic group from Ivalice. Vahn informs the King about Malacore and his plan, and the King allows them to check up on the Crystal of Wind while he consults with his strategists. Vahn and his party arrives at the Crystal Chamber in Wind Shrine where Malacore is already attending to the Crystal. The being orders the Necromancer to fight the dragoon and his party, but by defeating it the party is too slow to stop Malacore who has absorbed the Crystal's power. Malacore then challenges the party to a battle, intending to demonstrate his newly acquired power, but a voice interrupts him. Malacore recognizes the voice and identifies it as Darius, who has slept within Malacore. The fallen dragoon then taps into the Crystal power absorbed by Malacore and frees himself from the ties to Malacore and materializes before the entity is able to neutralize his consciousness. Darius then attacks Malacore with the power he attained from his ties to him and the being escapes, shortly after declaring its next target: the Crystal of Earth. Vahn decides to quickly go to Lindblum Kingdom and wonders if Darius will join him if he is not intending to return to Branch. Now the dark knight then says thay he wishes for nothing else and that he wants to pay back to Malacore for what he did to him. Just as the party leaves the Wind Shrine, Braak appears in the back noting how fruitful spying on Vahn and Vera has turned out. When the party returns, Lenadia Castle is under Ivalice attack and the group rushes to the throne room. In the throne room, Vahn comes across Braak, Deckar, and Eva and the blonde general reveals that Ivalice has suspected of something going on in Branch, hence his appearance there. Braak reveals that the Emperor wants to rule the world, seeing how Crystal power is powerful, and in order to achieve it he plans on conquering other lands. Appaled by hearing the generals' words, Vahn and his party fight and defeat them. Before teleporting away, Braak promises King Gorn that "this is only the beginning". The group retreats with the King to the conference room where they relay him the fate of the Crystal of Wind. During their conversation, Vahn reveals to King Gorn that apart of Malacore and Ivalice Empire, there are also Archareons who pose threat to them. The King says that the group shouldn't concern themselves with Ivalice for the time being as he will involve Lenadia in this matter, but also pursue alliance with other kingdoms. Darius then suggests going to Lindblum to to prevent Malacore from absorbing the Crystal of Earth. Back in Cornelia, Vahn enlists Cid to help him and his group travel to Lindblum.
After arriving in Lindblum, the party goes through the Cave of Dreams. Deep within the cave, most of the party suddenly falls asleep, with the exception of Ami and Nobumasa. In the dreams, Vahn appears in his hometown of Valla. He talks with his mother Elise who informs him that a dinner will be soon and Vahn decides to look around town. When he returns home, he says he has helped a girl find her doll and when he starts to inquire her about his father, Elise refuses to speak about it and the dragoon steps out of the house. When he enters the Elder's house and asks him about his father, the Elder assumes a monstrous form and multiplies across all over the house, promising him to tell Vahn provided he will stay forever in the town. Another dream takes Oalston back to Trei, in a setting where Malacore was defeated. Everyone is hateful towards Oalston and when he inquires the doctor about it he learns that he has murdered Maria. The guard then arrive and with the help of Doctor Cunnings they strip him of his power and imprison in his own house. Next dream takes Darius back to Branch, also after Malacore's defeat, where he returns to former glory and is assigned the role of general. Lord Adder orders him then to go to Meksicburg and slaughter anyone who does not show any respect for the dragoons since the townsfolk does so on regular basis. Darius is surprised by Lord Adder's course of actions, but he intends to carry the order out after the Lord's harsh words. From the other dragoon Darius learns that Lord Adder plans to launch an assault on Ivalice, and the dark knight decides to look for Vahn and Hans hoping they would talk some sense into their leader. He finds them in the dungeon where they inform Vera of her incoming execution and Darius decides to save her, only to be attacked by Vera. Hans and Vahn then turn into humanoid dragons that intend to put him to sleep. Elina's dream world is set in Mystic Mysidia's Elder's house where she writes a letter to her mom about how everyone praises her progress in styding white magic, however she feels insecure about her abilities. In the town she comes across ghosts disgusted by her. Back in the Elder's house she comes across Vartz who mocks her and reveals that because of her lack of abilities she couldn't save anyone and now is alone. Another dream world takes place in Albrook where Vera is hunted down by Ivalice soldiers, who upon seeing the situation in town decides to go to Branch and see Vahn. However as she is about to leave the town, she is strangely teleported to its entrance once again and falls asleep. Siegfried's dream takes place in a forest where he is searching for the Excalibur. Deep within the forest he comes across an old fisherman who reveals that the "Excalibur" is just a fishing hook and when Siegfried faints, the old man is joyful with the other man's failure. Back in the Cave of Dreams, Ami tries to persuade a creature to stop its doings, but Nobumasa urges her to take action, fearing for their comrades. The two defeat the demon and their friends wake up. Hearing from Nobumasa about the creature, Vahn urges the party to quickly leave the place, fearing that more monsters of that kind might be still in the Cave.
Arriving in Lantz, the group learns from the town Elder that a rebellion has grown in Lindblum, mainly fueled by the unrest caused by the Regent's priority on increasing the Kingdom's economical value. The rebels frequently destroy bridges that connect Lantz to western Kingdom and Vahn and his party volunteer to talk to the rebels and convince them to stop their actions. The party then departs east, on a newly rebuilt bridge to find the rebel base. While resting at the inn, Vera invites Vahn to a stroll across the riverbank and the dragoon takes her upon the offer. During their walk, Vahn expresses his doubts about being able to save the Crystal of Earth before Malacore absorbs it and Vera calms him by saying that as they travel the world they are also enlisting help of kingdoms' leaders and that Malacore has no way to win against that meny people. Suddenly a group of rebels appears and the two quickly dispatch them before they destroy it. After they return to Lantz to speak with the Elder, they comes across a group of rebels in his house and dispatch them. They then go after the Elder to rebels' hideout. Vahn successfully rescues the Elder in Rebel Hideout and they return to Lantz. With the Elder back in town, the western bridge leading to western Lindblum is rebuilt and the party continues on their journey. Coming to Surgate Waystation, Vahn tries to enter the lone building hoping to buy some supplies, but seeing how it is closed he decides to do it in the next town. As he is about to leave the place, several rebels come in an overwhelming number. Not wanting to fight a lost battle, Vahn notices a chocobo pen and escapes on one of the birds. As they are making their way through the rebels, Vahn is hit by a lightning spell and he and chocobo collapse. When he get up, he encounters Hans. The party fights the rogue dragoon and defeats him, but he teleports away. Some time later the party arrives at the Mage Academy and upon Oalston's suggestion they decide to stay there for a bit, while he and Elina explore and possibly learn something new. Oalston comes across Anders, who informs his fellow mage that non-elemental magic exists, surprising Oalston. He offers to teach him Comet after passing three tests administered by other people living in the Academy, first being Brawn, second Walter, and the third by Balthier. Overcoming their trials, Oalston returns to Anders who challenges him to complete all three trials in a single battle. Winning the battle, Oalston learns Comet from a book. Meanwhile searching for help, Elina comes across Lyon who directs her to Sabino. He challenges her to a trial in order to get a new spell by testing her ability to switch between offensive and defensive tactics. Winning the battle earns Elina right to learn Prayer.
Arriving at Lindblum Castle, Vahn speak with Regent Gran and warns him about the danger that awaits the Crystal of Earth. The Regent says that he knows about it and is currently working hard trying to reclaim it. Asking if it was Malacore's doing, Regent Gran says that this is the first time he hears about such entity and says that the Fen of the Underworld have stole the Crystal. He reveals that two nights ago the Fen has come to Mt. Koltz where the shrine to the Crystal is located, breached to its Chamber, and after escaping to the Underworld with it they sealed the way with a powerful magic barrier. Hearing about difficulties that Lindblum mages have with disabling the barrier, Oalston, Elina, and Vera volunteer to help them and are escorted by the soldiers to aid the mages. With the three gone, Regent Gran asks Vahn and his remaining allies to help him stop the rebellion led by Baram. Vahn agrees and is tasked with liberating the town of Dawnmarch from rebels. Regent Gran arranges a chocobo for him, allowing the group free travel across the continent.
A year after the Great Cataclysm, Oalston goes to Lindblum and constructs a new mage academy. Oalston achieves world fame as the most skilled mage in the world and many people would come to him seeking his guidance. At the age of 72, Oalston starts to teach a 10-year-old Hautley von Muir black magic despite the boy's concern for Oalston's health in case he would hurt his teacher. Thanks to him, people start to trust black magic again.
- Note: Abilities are listed horizontally as learned through leveling.