For the sake of convenience, the Player Character will be referred to by their canon name of "Robin" and with male pronouns.
Neighboring the Archanea continent was another continent named Valentia, split between two kingdoms who worship two exiled Divine Dragons: Rigel, patronized by Duma the War Father, and Zofia, who worships Mila the Earth Mother. The two kingdoms were also embroiled in war, but thanks to the efforts of Alm, heir to the Rigelian throne, and Celica, the lost Zofian princess, Mila and Duma were laid to rest for good, and the two kingdoms were reformed into a single kingdom.
Meanwhile, in Archanea's Mamorthod Desert, there was a city known as Thabes. Once a golden city of knowledge, Duma grew fearful of the humas' power in it, and destroyed it after a three day war, resulting in his and his sister Mila's exile from Archanea into Valentia. Underneath the city during its glorious days was a Labyrinth, and lurking in it was a mad alchemist named Forneus, who sought to create the perfect life form and a way to bring the dead back to life. Using materials that include the blood of the Divine Dragon, Forneus managed to create a life form on the size of a fetus. It grew into a peculiar creature, having six eyes. As the creature matured, Forneus began to see through its mind and saw only hateful and destructive impulses. Eventually, Forneus decided that the creature could not be controlled and must be destroyed, but this creature, only dubbed as "the Creation", proved to be too powerful, and Forneus was slain.
Word of the Thabes Labyrinth soon reached the ears of both Alm and Celica. Gathering their most able men, they traveled to the Labyrinth, where they come across writings from the Thabean Senate, who had sealed the Labyrinth after hearing word of Forneus' activities, as well as writings of Forneus himself. Inside, they witnessed the might of the Creation, as well as the other results of Forneus' experiments: reanimated beings that had risen from the grave. Combining their strengths, Alm and Celica seemingly defeated the Creation and the zombies. However, they noted that the Creation's malevolent presence, filled with dread, continued to linger within the place, which would never fade away. For the moment, Alm and Celica stopped that threat and resumed their lives, but the Creation would return in a time far in the future.
Years after the formation of Ylisse, the Creation would return, in the form of a terrifying dragon, now dubbing itself Grima, the Fell Dragon. The Divine Dragon Naga, however, was still around. With the help of the First Exalt of Ylisse, she fought against Grima and put it in a long slumber. However, before his slumber, Grima has attracted a cult of worshippers, calling themselves "the Grimleal", which formed the theocracy of Plegia, becoming rivals with the Naga-worshipping Ylisse as they worked for the return of Grima.
All seems well, at first. As Chrom helps Robin to his feet, however, a dark force suddenly takes over Robin's body, forcing him to stab Chrom in the chest. Mortally wounded, Chrom assures Robin that he is not at fault as he collapses upon the floor, dead, and a burst of evil laughter fills the room...
On their way to the village of Southtown, however, they find it being ransacked by bandits. Chrom and his fellow Shepherds immediately rush in to fight them off, while Robin decides to join the fray shortly afterward. As it turns out, Robin is not only handy in a scrap but also has an innate knack for battle tactics. He and Chrom both lead Lissa and Frederick to victory against the bandits and drive them out of town.
When the dust settles, an impressed Chrom is convinced that Robin has a good character, and offers him a spot as the Shepherds' tactician, which he accepts despite Frederick's lingering concerns of his trustworthiness. On another topic, Frederick shares with the others that he noted a distinct accent among the bandits, suggesting they came from Plegia, a kingdom neighboring Ylisse's western borders. Plegia has long desired war with Ylisse and is known to send bandits in the hopes of instigating conflict.
With Southtown saved, the villagers offer a feast in honor of their saviors, but to Lissa's chagrin, Frederick insists that they must return to Ylisstol, the capital of the Halidom, as soon as possible. Thus, the Shepherds and Robin set out once more...
In the middle of the night, Chrom and Lissa wake up with a strange feeling that something is amiss and head off to investigate. From out of nowhere, an earthquake causes lava to erupt from the ground, forcing the siblings to flee. Their respite is cut short, however, by the opening of a mysterious portal in the sky and the appearance of two undead warriors who attack them fiercely, with one of them cornering Lissa. They are saved, however, by a young man, his face concealed by a mask, who also appears from the portal and fends off these undead zombies.
As the forest becomes engulfed in flames caused by the erupting lava, more of the deathly creatures appear. Robin and Frederick soon arrive, where they later get more help in the form of Sully, a brash tomboy Shepherd; and Virion, a mysterious archer who doggedly pursues women's affections.
After the battle, the young man introduces himself as "Marth", taking his name from the Hero-King of Ylissean legend. He warns Chrom that what they saw was but a prelude to a greater calamity before taking his leave.
The Shepherds and Robin arrive in Ylisstol upon daybreak. While making their way through the city, the ruler of Ylisse, the Exalt Emmeryn, appears to greet the townsfolk. Lissa reveals that Emmeryn is her older sister, meaning that she and Chrom are a princess and a prince!
The revelation shocks Robin, who wonders why Chrom and his companions would refer to themselves as "shepherds". Chrom explains that his "flock" is the people of Ylisse: they fight to defend them.
With that out of the way, Chrom and the others meet with Emmeryn in the palace to relay the news of Plegian bandits attacking villages and the appearance of the undead creatures, as well as Robin's induction into the Shepherds. After introductions, Emmeryn tells Chrom that she is holding a council on the matter, and the prince agrees to join, along with Frederick and Phila, a pegasus knight serving as the Exalt's retainer, while Lissa and Robin take their leave.
The group set out, and are joined shortly afterward by Stahl, a cavalier with a big appetite. As they make their way north, however, they are beset by the undead monsters, which the Ylissean war council had dubbed "Risen". Reinforced by Miriel, a studious if deadpan mage, they manage to fight their way past the Risen.
As they continue their trek, the Shepherds come upon a wounded pegasus. Chrom's attempts to aid it are met with resistance from the winged stallion, but Sumia reveals her knack for caring for pegasi. She stays behind to tend to its wounds while Chrom and the others march on.
Eventually, Raimi relents; recognizing Chrom's claim to be of Ylissean royalty as genuine, she permits him and his Shepherds entrance into Regna Ferox.
In the tournament, Chrom again encounters "Marth", who is fighting as one of the champions of Basilio, the West-Khan and current ruler. To Chrom's surprise, the sword Marth wields looks exactly like his own Falchion! Marth claims he had learned to fight from his father, and he and Chrom prove an even match for each other. In the end, however, Chrom emerges victorious, as does his Shepherds.
Flavia, now sovereign of Regna Ferox, officially agrees to lend soldiers to Ylisse's defense. They are greeted by Basilio, who mentions that Marth has up and vanished after the tournament. In respect of Chrom's martial skills, the West-Khan lends his best soldier to Chrom's Shepherds: Lon'qu, a swordsman from the far-away island nation of Chon'sin.
Chrom and the Shepherds return to Ylisse to relay the good news to Emmeryn. There is little time to rejoice, however: Phila's recent reports reveal that Plegian soldiers had crossed the border into Ylisse, attacked a village in Themis territory, and taken Maribelle captive! What's more, the ruler of Plegia, the Mad King Gangrel, has claimed Maribelle crossed illegally into his kingdom! Chrom wishes to kill Gangrel and be done with him, but Emmeryn, wishing to avoid conflict, insists that she meet him at the border and try to parley. Chrom and Phila agree to allow her to go but insist that they and the Shepherds escort her.
Before Maribelle could come to harm, she is rescued by Ricken, a young mage-in-training. With the blood already shed, a satisfied Gangrel declares war upon Ylisse and leaves his captain, Orton, to deal with the Shepherds. The Shepherds succeed in fighting off Orton and his forces and, with Maribelle safe, return to Ylisstol to discuss how to proceed with the coming war with Plegia.
Chrom and Robin are approached once more by Marth, who warns them that the Exalt was in danger of being assassinated this very night. To prove the veracity of his claim, he warns Chrom of assailants waiting to attack him at that moment. Marth and Chrom fend off the assassins, but Marth's mask is broken in the fighting, and it is revealed that "he" is actually a young woman!
An explosion rocks the palace shortly thereafter as assassins, led by a foul sorcerer named Validar, break into the palace to take the Fire Emblem and kill Emmeryn. Among the group of assassins is a noble-hearted thief with a Sweet Tooth named Gaius, who is reluctant to kill the Exalt. Chrom can persuade him to switch sides by speaking to him (with a little help from Lissa's bag of sweets which he's carrying in his pocket). Joining the fray later in the battle is Panne, the last of a race of shape-shifting beast-people called the Taguel. Marth reveals her to be an ally, so Chrom orders the Shepherds to let her be.
Eventually, the Shepherds drive off the assassins, and Validar is slain. With Emmeryn safe, Chrom seeks out "Marth". She takes her leave, content that Emmeryn's safety had averted the series of events that had led to the realm's ruination. Back in the palace, Panne, while apprehensive to humans, agrees to join the Shepherds out of gratitude to the Exalt's willingness to ask forgiveness for the genocide of the Taguel race. With the safety of the royal palace compromised, arrangements are quickly made to escort Emmeryn to a hidden eastern palace for safety while Chrom and the Shepherds petition Regna Ferox for additional aid.
All the while, Validar finds himself in a dark void, where he is approached by a mysterious figure calling himself "Grima"...
Chrom fends the Plegians off, but in the fighting, Plegian soldiers storm Ylisse's borders. Cordelia, a prodigious pegasus knight who bears unrequited feelings for Chrom and the last of her squad to survive Gangrel's onsaught, arrives to warn them of the incursion.
Emmeryn and Phila decide to return to Ylisstol, despite the danger and Chrom and Lissa's pleas, to bring hope to the people. Before leaving, the Exalt entrusts Chrom with the Fire Emblem and instructs him to take it to Regna Ferox for safety.
In Ferox, the siblings wrestle with grief and worry. Lissa frets about openly, but Chrom remains distant. Sumia, in an honest effort to snap him out of his funk, punches him across the face, to the amusement of the arriving Flavia. The East-Khan informs them that the Feroxi army is ready to mobilize, as per the deal with Ylisse, and that she is joining the fray herself, with Basilio in tow.
Unfortunately, Basilio shows up with terrible news: the scouts have reported that Ylisstol has fallen! Emmeryn has been captured, and King Gangrel intends to put her to death within the month! Chrom vows to save her, and Robin agrees to lend his aid.
With no time to waste, the Shepherds cut through Chalard and his men, while keeping three nearby villages out of harm's way. With the villainous men disposed of, the misunderstanding is cleared: Nowi had been enslaved by brigands, but Gregor decided to free her, only for them to be pursued by the evil men seeking to sacrifice her: the Grimleal, a fanatical cult worshipping Grima, the Fell Dragon who terrorized the world before the First Exalt of Ylisse defeated him a thousand years ago. To prevent Nowi from going back to the auction board or falling into Grimleal hands, the Shepherds agree to enlist her and Gregor into their services. With the pair's issues solved, the army takes a rest on Flavia's suggestion, as the Plegian capital is near.
The next day, the Shepherds march on to the Plegian capital as Emmeryn is put on the chopping block at the top of a cliff. A melee breaks out between the Shepherds, who are joined by Libra, a war monk often mistaken for a woman and the last survivor of a group of clergymen heading to Plegia in order to help the rescue, against the Plegians, including Tharja, an apathetic and antisocial dark mage with a jealous streak, who switches sides if Chrom, who notices her reluctance, invites her to join.
The battle soon swings in the Shepherds' favor, signaling the arrival of Phila and her pegasus knights, but their momentum is halted when Aversa summons a group of Risen archers, which proceed to kill Phila and her squad. With the tide turning in his favor and the archers pointed at Emmeryn, Gangrel makes his ultimatum: relinquish the Fire Emblem, or the Exalt dies!
Before Chrom could act, however, Emmeryn makes a bold gesture. She calls out to the Plegians and begs them to release their hatred and break free from the cycle of violence and vengeance as she does what she must to change the world. With her final thoughts being those of love for Chrom, Lissa, and her people, she then falls from the cliff and to her apparent demise, while the Ylisseans could do nothing but watch in horror...
An enraged Chrom declares Gangrel a dead man walking, but before he can exact revenge or retrieve his sister's body, Basilio warns him of more soldiers inbound. With the mission a failure, the Shepherds make a reluctant retreat, a dark cloud looming above them all.
From the shadows, "Marth" is powerless to do anything but watch, lamenting that she arrived too late. The grim future ahead is set on course once more...
Mustafa, sympathetic to the Ylisseans and touched by Emmeryn's words, offers to grant them mercy if they surrender. The Shepherds, however, are unwilling to trust his word and rally themselves to arms.
As the battle continues, several Plegian soldiers become reluctant to fight, themselves also touched by Emmeryn's sacrifice. Mustafa dismisses anyone unwilling to fight any further, but he himself would not leave, for the price would be to lose his wife and child. The general's words inspire his men to continue fighting for a different cause: loyalty for him.
Mustafa fights valiantly, but he is eventually struck down; his final request is only that Ylisse would spare all of his surviving men. With the battle won, the Shepherds make their escape to regroup in Ferox, with the help of a particular woman close to Basilio: Olivia, a shy but talented dancer.
In Castle Ferox, the Shepherds lament the loss of their Exalt. Chrom in particular felt powerless, unable to do anything to save his sister. He doubts that he could live up to her, but a few choice words from Robin and the rest of the Shepherds convince him otherwise. His resolve strengthened by their encouragement, Chrom knows what to do next: stop Gangrel, and avenge Emmeryn. Olivia, seeking to honor a debt of gratitude to the Exalt, offers her assistance as well, and the Regna Ferox khans affirm their support in putting an end to Gangrel's tyrannical reign. Renewed, the Shepherds march forward to stop the Mad King once and for all.
As the Shepherds approach the Border Wastes, ready to dethrone Gangrel once and for all, Frederick bids tidings from Flavia: the Plegian army is fractured from infighting and desertion. Chrom surmises that the deserters are dissuaded from fighting by Emmeryn's sacrifice, a notion which Frederick confirms. Realizing that Plegians also seek peace, the Shepherds March to defeat Gangrel and return peace to both Ylisse and Plegia.
Gangrel, more than ready for one last battle, stands by himself. He taunts Chrom over the loss of his sister while comparing themselves as not-so different from each other, but the prince, confident with his brothers-and-sisters-in-arms by his side, refuses to be disheartened. Thus, the final battle of the war begins.
Despite Plegian reinforcements, the Shepherds, with the help of Olivia and her spirit-renewing dances, manage to come on top and defeat Gangrel. The Mad King falls with one last taunt to share:
And so, the second Ylisse-Plegia War is over. The daunting task of leading the reconstruction of Ylisse lies ahead of Chrom and Robin, for the war had taken a great toll on the populace, but with the help of Regna Ferox as well as the reparation gold from Plegia, the Halidom stirs back towards recovery. In the meantime, the prince refuses the title of Exalt, in the memory of his sister. Soon after, the royal wedding is held, and it is a joyous moment to all. At last, the lingering wound of history seems to have been healed.
Two years later, however...
An urgent message from Flavia arrives in the form of Raimi: the western continent of Valm, renamed after the first ruler of the unified continent of Valentia, Alm the Saint-King, is no longer acting to the best interests of Ylisse. The Khan Regnant wishes to meet with the prince personally, a motion Chrom agrees to. Before departing for Ferox, Chrom meets with his wife, along with their newborn baby: a daughter named Lucina, who bears the Brand of the Exalt in her left eye (much like Chrom bears his in his right arm's shoulder). If Chrom had married the maiden, she reluctantly accepts his choice to depart while she stays, as she knows nothing of combat. Otherwise, his wife objects to the prospect of staying, since Lucina can be left with a wet nurse while they are in Ferox, to Chrom's reluctant agreement; if he had married Olivia, they share a brief reminiscence of his proposal before leaving.
In Castle Ferox, Flavia greets the Ylisseans and informs them that while the Valmese fleet is moving towards the continent of Ylisse, not much else is currently known. Basilio enters the scene with a familiar face: Virion the archer. As it turns out, he is a duke! His retainer, a wyvern rider with an odd sense of aesthetics named Cherche, reveals that they hail from the Valmese country of Rosanne. They have escaped in order to recruit new allies to fight against the eponymous country of Valm, which has transformed from a pitifully small kingdom to an empire, all thanks to its Emperor: Walhart, the Conqueror. With all of Valm under his control, Walhart has now set his eyes upon Ylisse; his fleet is due to arrive in a matter of days. With Virion's advice, the Shepherds prepare for a battle against a strong cavalry force.
With the help of Cherche and her wyvern Minerva, the Shepherds prevail over Dalton's forces, but it quickly becomes apparent that both the town surrounding the port and the Feroxi army is in shambles. This does not bode well for everyone, as Feroxi soldiers are known to be the finest troops of the eastern seas. Worse, the forces they had just repelled was merely an appetizer: a much larger fleet is on the way. And once they arrive on shore, there would be no way for Ferox or Ylisse to repel them. Robin notes that Valm's greatest asset is their land cavalry, so they need to neutralize that advantage by attacking the Valmese at sea. But neither Ylisse nor Ferox owns any warships on the western border, which means they will need aid from one which does have them, as well as the funds needed to sustain a counterattack: Plegia. Chrom refuses at first, but relents after some persuasion from Basilio, Flavia, and Robin.
Soon enough, Frederick informs the prince that Plegia agrees to meet them in Carrion Isle, an island to the south. Not an advantageous location in the event of negotiations going sour, but Chrom is certain that Plegia will want to help, since Valm is as much of a threat to them as it is to everyone else. Hopefully, the new king will be of more help to them compared to Gangrel....
That night, as the Shepherds travel across the Plegia highroads, Robin is left feeling troubled by the thoughts of the Hierophant. But from out of nowhere, he hears the Hierophant's voice, before a headache suddenly consumes him. from which Validar's voice comes out. The king reveals himself to be Robin's father, and demand that he give himself up to "him": the Fell Dragon, Grima. However, Chrom, who overheard his friend's shout, enters the scene, forcing Validar to drop his connection. His headache dissipating, Robin proceeds to inform Chrom of what Validar told him, and the prince speculates that the Hierophant may be a twin brother, though Robin himself is unsure. But Frederick comes in with troubling news: despite the posted sentries guarding them, they are now under Risen attack! Chrom curses Validar for enabling it, then prepares the Shepherds for battle.
With the help of Henry, a disarmingly optimistic Plegian dark mage with a love for blood and a near-perpetual grin, the Shepherds manage to kill the Risen Chief leading the ambush. But from out of nowhere, a Risen assassin appears, attempting to kill Chrom, only to be blocked by the arriving "Marth". But in the process, she accidentally refers to Chrom as "Father". With nowhere else to go but for the truth, she requests a private audiance with him, where she asks him to look at her in the eye. What he sees in her left eye makes her true identity and relationship to him clear:
Lucina reveals where she hails from: a dark future where the Fell Dragon, Grima, was resurrected. Chrom and all of his Shepherds were killed, and the world stood on the brink of extinction. Chrom takes her bearing the Archanean Falchion, a unique weapon in and by itself, as well as Lissa's testament to her arrival from the portal back in the forest, as sufficient proof, while his wife, now fully convinced, accepts Lucina as her daughter, and they share a tender moment together. If Chrom is married to the maiden, he and Lucina will instead share a moment to talk about the latter's infant self, as well as her mother.