Do you know what the Butterfly effect is? It's the idea that small causes can have large effects further down the road. Like where a butterfly flaps its wings in one place which can cause a hurricane elsewhere. You can't see the effects it will have further down the road when you make a choice but you can't change things once you made that choice. The more important of a choice it is, the bigger the impact it will have on the world around you. The choice of one young man, when a war is born between two warring nations, has consequences that perhaps no one could have forseen. Kamui, a young prince, raised by Nohr but born to Hoshido, has this choice thrust upon him following the death of his mother Queen Mikoto. When his family from Hoshido and Nohr come together, he is forced to choose Hoshido and his blood siblings or Nohr and his adopted siblings.

Choosing the path of his Birthright, Kamui aided his blood siblings Ryoma, Hinoka, Takumi and Sakura and other loyal Hoshidans in defending Hoshido from invasion by Nohr. The time came, and Kamui led his family to Cheve where they were reunited with Ryoma and where Kamui met the woman whom he would fall in love with, Scarlet the leader of the Cheve resistance. However, following this would be a string of deaths including Flora and Lillith and Kamui swore that King Garon would pay for all the deaths he orchestrated. Confrontations with both Leo and Camilla fortunately came out favourably with no sides losing lives. With the help of Elise and a man named Shura, they were able to invade Nohr's capital. However, Kamui was forced into one-on-one combat with Xander, and when Elise tries to stop the fight, she is mortally wounded by Xander. In his grief, Xander forces Kamui to face him and kill him. Finally Kamui and the Hoshidan army is able to face off against Garon. The Yato, the sword which Kamui had been chosen by, resonated with the legendary weapons of Hoshido: The Fujin Yumi and the Raijinto, held by Takumi and Ryoma respectively. Though they managed to injure Garon, he succeeds in destroying the yato and almost killing Kamui. The voices of both the living and the dead gave Kamui the power to wake up and reforge the Yato. Finally managing to kill the Garon, who had taken on the form of a monstrous dragon, Kamui learns from Garon that he has in fact been dead for a long time. However Kamui and the rest of the Hoshidans are not given much time to comprehend this. This is because Azura, who had been singing her song throughout the battle, was dying, dissolving into water. With a last request for them to smile for her, she passes away becoming water vapour and evaporating. Time passed, peace now restored to Hoshido and Nohr. Ryoma had been crowned King of Hoshido while Leo has been crowned King of Nohr. Under the statue of their mother, Kamui and his siblings vowed to continue their work for peace to the world.

However this was not the only path that Kamui could have chosen to walk. In another, very similar world, Kamui chose the other path, the path of Conquest. Kamui now aids his adoptive siblings Xander, Camilla, Leo and Elise not only in the war against Hoshido but in changing Nohr from the inside, to change Nohr's brutal reputation. While on missions from King Garon, he is temporarily reunited with Flora whom he would later marry after she joined the army. After Azura, who joined Nohr after some Hoshidans kidnapped her and turned on her, reveals the true nature of King Garon, having been replaced with an imposter, Kamui decides that he has to have Garon sit on Hoshido's throne which had the power to reveal the truth. It would remove the false Garon's disguise but for this plan to work, Nohr would have to conquer Hoshido. During the invasion of Hoshido, Hinoka is spared while Sakura is taken captive. Takumi also appears to commit suicide, whose behaviour has been oddly erratic throughout the course of the war. Garon orders Kamui to kill Ryoma who, after their fight, chooses to take his own life instead of allowing Kamui to suffer the agony of killing him. After this, Garon is revealed to be and imposter who had orchestrated the whole war, in an attempt to destroy Hoshido and Nohr. As with the Birthright path, the Yato resonated with the legendary weapons of Nohr: The Brynhildr and the Siegfried, held by Leo and Xander respectively. Kamui was able to kill the false Garon but following his defeat, Takumi reappears possessed by some unnatural force and attacks Kamui. Spirits of the dead, including Takumi whose has been dead for some time, help Kamui return and kill Takumi's body so his soul can be released. Azura, who had been singing during the battles, has died as well but no one realised it so she is considered missing and not deceased. Time passes, Xander is crowned King of Nohr while Hinoka becomes the Queen of Hoshido. Together with his adopted siblings, Kamui works for peace in the world, between Hoshido and Nohr and a better future for Nohr.

However, there was another choice Kamui could have made and again, in another similar world to the first two, Kamui had to make a choice and again he chose differently. This time Kamui chose to side with neither Hoshido or Nohr, unable to raise his blade against either set of his siblings. After leading a small group to defeat the lead commanders of both Hoshido and Nohr, he is proclaimed a traitor and is forced to flee with both Azura and Jackob. Azura takes them to Valla through the Bottomless Canyon and shares the secrets of Valla as well as allowing them to reunite with Gunther. Kamui and Azura together resolve to unite Hoshido and Nohr and end the war before the skies change and seal off the passage to Valla and kill Anankos, who is behind this war. At some point during their travels, Kamui meets and eventually marries Mikoto's former retainer Reina. During Kamui and Azura's journey to recruit Hoshido and Nohr, they learn that the Yato is the 'Seal of Flames' which if its power combined with that of the 4 other legendary weapons, it would become the Fire Emblem. The Fire Emblem had the power to kill Anankos. Ryoma and Xander, thanks to Kamui's actions, call a true between their nations to face their true enemy and finally Kamui is able to convince them to leap into the Bottomless Canyon and enter Valla. However tragedy strikes as Kamui is attacked by an unknown force and Scarlet sacrifices herself to save his life. Following their first battle in Valla, Ryoma learns of Scarlet's sacrifice and, while grieved by the loss of his friend, resolves to continue fighting. Finally, Kamui and Azura are able to fully explain the situation to the others and the two nations truly unite to take down Anankos. During their travels through Valla, the army encounters a number of resurrected and controlled humans including Arete (Azura's mother), Mikoto and King Sumeragi of Hoshido. While facing Mikoto, Kamui learns that he is in fact royalty from Valla to his surprise. It is discovered that Gunter is being controlled by Anankos and is in fact the murderer of Scarlet, but Kamui with help from Azura is able to free him of his control. Finally Kamui leads the forces of Hoshido and Nohr against Anankos with his sword The Yato having resonated with the 4 other legendary weapons. Anankos, in an attempt to recover his strength, summons and eats Garon. But he is still killed by Kamui, ending the war. Following the end of the war, Valla is reborn alongside Nohr and Hoshido on the surface. Azura abdicates from the throne and crowns Kamui in her stead and finally peace is restored to the three kingdoms.

During the war, members of the army married and had children who, until the end of the war, remained safe in their deep realms. After the war, they were brought from their deep realms to live with their parents. However something is stirring and a storm brews on the horizon…