Byleth was born of Jeralt and Sitri, a nun of the Church of Seiros in Imperial Year 1159, in critical condition and not breathing. Rhea took the Crest Stone of Flames from Sitri (who failed to achieve the progenitor god's conscience, and was also in critical condition) and placed it within the infant Byleth's heart, both to save the infant Byleth as well as to try again to reawaken the goddess Sothis; this resulted in Sitri's death. However, this had the consequence of Byleth having extremely little emotion until the goddess started to reawaken around the start of the game. Jeralt, seeing the infant's oddities and fearing Rhea's plans for them, took advantage of a fire to fake both their deaths and fled the monastery. The two spent the next twenty years wandering Fódlan as part of a mercenary troop.
One day, Jeralt's aid is requisitioned by three young nobles under attack by bandits: Princess Edelgard von Hresvelg of the Adrestian Empire, Prince Dimitri Alexandre Blaiddyd of the Holy Kingdom of Faerghus, and Lord Claude von Riegan of the Leicester Alliance. During the battle, Byleth sacrifices themselves to save Edelgard from an attack; this awakens Sothis' consciousness within them, and she grants them the power of Divine Pulse to rewind time.
Afterwards, the Knights of Seiros reunite with Jeralt and convince him to return to the Church, where Rhea offers Byleth a teaching position at the Officers Academy at Garreg Mach Monastery. Byleth chooses one of three academic houses to lead: Edelgard's Black Eagles, Dimitri's Blue Lions, or Claude's Golden Deer, and spends the next year teaching them and fighting alongside them. During this time, a masked individual calling themselves the Flame Emperor and a cult known only as "those who slither in the dark" launch attacks on the Church. During a raid on the Church's Holy Mausoleum, Byleth discovers the Sword of the Creator and learns they possess the Crest of Flames, the Crest borne by the King of Liberation Nemesis in ancient history. Rhea entrusts the sword to them. Eventually, the assassin Kronya murders Jeralt; Byleth pursues her into the Sealed Forest outside Garreg Mach, falls into a trap, and is banished into a realm of darkness. Sothis sacrifices her individuality to grant Byleth the full extent of her power, allowing them to escape. In the aftermath, Rhea takes them to the Holy Tomb far underneath Garreg Mach to receive a divine revelation. The Flame Emperor interrupts the ritual to raid the Tomb, and in the ensuing battle is revealed to be Edelgard.
If Byleth is a Black Eagle and attended her coronation as emperor earlier that month, they can defect to the Empire; otherwise, they remain allied with the Church. Edelgard, who views the Church as corrupt due to propagating the worship of Crests which led to the deaths of her siblings, declares war on the Church and attacks Garreg Mach. The Empire wins the battle, and Byleth is severely injured and falls into a coma for the next five years.
If Byleth sides with the Church, they awaken to find that the Kingdom has been reduced to a puppet state, Dimitri is presumed dead, the Alliance has fractured into pro-Church and pro-Empire factions, Claude has been struggling to maintain a facade of neutrality, Rhea has been captured by the Empire, the Knights of Seiros have scattered to the four winds to find her and Byleth, and the Empire is on the verge of conquering Fódlan. Byleth rallies an army to combat the Empire, with the exact details varying depending on the route. After a massive three-way battle between the Empire, Kingdom, and Alliance known as the Battle at Gronder, Byleth directly invades Adrestia and conquers Fort Merceus, a critical stronghold on the path to the Imperial capital of Enbarr. They then launch a direct invasion of Enbarr itself, and kill Edelgard. On the Azure Moon route, the war ends here; Dimitri and the Kingdom unite Fódlan under the former's rule, and Byleth becomes archbishop of the Church after Rhea retires. On the Silver Snow and Verdant Wind routes, Hubert posthumously warns them about those who slither in the dark, and Byleth besieges their stronghold Shambhala and kills their leader Thales. After defeating either Rhea after she suffers a draconic degeneration-induced mental breakdown due to injuries sustained in Shambhala (Silver Snow) or Nemesis after he is resurrected by those who slither in the dark as a last act of spite against Fódlan (Verdant Wind), Byleth unites the continent as the first ruler of the United Kingdom of Fódlan.
If Byleth sides with the Empire, they awaken to find that Dimitri has granted Rhea asylum and sided with the Church, and the two of them have fought the Empire to a stalemate while Claude and the Alliance remain nominally neutral. Byleth and Edelgard launch a renewed offensive, conquer and annex the Alliance, and either kill or exile Claude. After beating back a counterattack by the Church and assassinating a high-ranking member of those who slither in the dark, Byleth launches a direct invasion of Faerghus. Dimitri and Rhea intercept them at the Tailtean Plains, but the Empire emerges victorious, Dimitri is slain, and Rhea is forced to retreat to the Kingdom capital of Fhirdiad. Rhea orders Fhirdiad to be burned to the ground to slow the Imperial advance, but Byleth nevertheless defeats her and brings an end to the war. In the aftermath, Rhea's death causes the Crest Stone implanted in Byleth's heart to disintegrate, allowing their heart to start beating normally for the first time. Edelgard and the Empire unite the continent under the former's rule, and Byleth takes up arms against those who slither in the dark as their shadow war begins.