Nemesis is an ancient king of Fódlan who took over the continent over 1200 years before the start of Fire Emblem: Three Houses. Nemesis is a legendary figure that is remembered as an agent of the Goddess Sothis who was blessed with the Crest of Flames and the Sword of the Creator to fight against "Dark Gods" before turning against her and seemingly being killed by Saint Seiros, her new champion.
In reality, Nemesis was the leader of a group of thieves working for Those Who Slither in the Dark who managed to infiltrate her resting place and killed her in her sleep. Nemesis then infused himself with her divine powers by drinking her blood thus gaining the Crest of Flame and took her bones to make the Sword of the Creator. This is why he was put down by Seiros. After his death, his corpse was recovered by Those Who Slither in the Dark who worked on reviving him for the next thousand years thus resulting in his return in the Verdant Wind route where he serves as the final Boss.
Nemesis was born several decades before the year -41, which is the earlier year of reference we have. By that time Nemesis had already killed Sothis and infused himself with her divine blood giving him incredible longevity and the Crest of Flame as plotted by Those Who Slither in the Dark. After killing Sothis, Nemesis and his group of thieves used his newfound powers to slaughter the Nabatean in Zanado and used their blood and bones to infuses their whole group with power and longevity and create other weapons.
The only survivors of the tragedy was Seiros herself who was traumatized by the death of her peers and the four saints who were supposedly away at the time. Nemesis then ruled the continent uncontested for an unknown amount of time and people were encouraged to follow his methods and attain power by any means necessary. Seiros revealed herself to humanity in -41 and form the Church of Seiros around herself and the revelation she claim to have been given to oppose Nemesis' rule. In the year 1 the Adrestian Empire was founded around the city of Enbarr by Seiros and the newly appointed emperor Wilhelm I to oppose Nemesis. Wilhem I is given Seiros' blood to seal their alliance and the Emperor's bloodline inherits the Crest of Seiros as a result. The emperor himself would live an abnormal long time.
In 32, the influence of Wilhelm I grew to such an extend that he is powerful enough to officially declare war to Nemesis and his followers with the goal to unify Fódlan. In 46, the war has grown to such an extent that Nemesis and his ten Heroes themselves start to fight the empire's army. The Battle of Gronder happens and marks a decisive victory for the Empire. In 91 Nemesis is killed during the Battle of Tailtean. The war officially ends in 98 when Lycaon I, successor of Wilhem I, dies of sudden illness. The bloodlines of the Ten Elites are then put into power in the empire as a way for Seiros to keep a certain control over the power of her peers that began to spread when the Ten Elites had children. To avoid having the power of the Crest spreading everywhere and appearing in random individuals who could eventually become as dangerous as Nemesis, the nobility was born. Those Who Slither in the Dark then obtained his body through unknown means and spent the next 1000 years trying to ressurect him.
Seiros then twisted history through the church to protect the peace of the continent. In her version, Sothis didn't die but left the continent for the heavens to watch over its people. Crests were a blessing given by the Goddess to humanity to defend themselves against "Dark Gods" who had threatened Fódlan in the past. Nemesis was a Hero who was corupted and betrayed the Goddess and the Ten Elites were never on his side but fought alongside herself and the four Saints in the war.
In the year 1180 Byleth Eisner, the newly appointed professor of the Officers Academy, was tasked with subduing thieves in the Holy Mausoleum during the Goddess' Rite of Rebirth. The thieves were sent to gather crest stones and steal the Sword of the Creator who was hidden in Seiros' supposed tomb since the defeat of Nemesis. It was revealed that Byleth had the Crest of Flames through his ability to use the Sword of the Creator. Rhea, the archbishop of the Church of Seiros then tell Byleth who Nemesis is and what the Crest of Flames he possess represents. She of course give him the false version crafted by the church. Later, professor Hanneman von Essar confirms that it is indeed the Crest of Flames and that Byleth must be the descendant of Nemesis himself. This is questioned a lot because Nemesis is known to have left no children during his long life.
In this route, Rhea who reveal herself as Seiros tell Byleth the truth about his crest and explain to him Nemesis' true role in the war. His crest comes from Sothis' Crest Stone, which is her heart, that was taken from the Sword of the Creator after Nemesis fell and then implented in multiple vessels in the hopes of creating one suitable for Sothis. Byleth and their mother were both vessels and Byleth inherited it from her mother after she told Rhea that she was willing to sacrifice herself to give the Crest Stone that served as her heart to her dying newborn.
Before departing to Derdriu, Edelgard von Hresvelg reveals to Byleth that Nemesis was never corrupted and that Seiros manipulated the people of Fódlan to wage war against Nemesis. This knowledge was passed down from emperor to emperor, as Wilhelm I was an ally of Seiros during the War of Heroes. This is only partially true however as Nemesis rulled as a tyrant and had been known to crush everyone who stood in his way with his incredible power. Edelgard fails to mention that this was done to protect Fódlan from repeating what was basically over a century of attrocities.
After Claude von Riegan, Byleth, Rhea and their allies raid Shambhala with the goal to kill Thales, the leader of Those Who Slither in the Dark, Nemesis and the Ten Elites are finally resurected by Agrathan technology as the city was crumbling due to Thales' final suicide attack.
Soon after, it is repported that the remanants of Those Who Slither in the Dark where reported to have been marching toward Garreg Mach Monastery led by a force of eleven men with incredible powers who were slaughtering villages as then marched forward. The leader of the army is eventually identified as Nemesis and Claude sees this as an opportunity to end Fódlan's bloody history once and for all. The army was intercepted at the Caledonian Plateau and the final battle with Nemesis ended with his defeat at the hands of Byleth and Claude after the Ten Elites were finally killed.