Never ones to let an opportunity pass them by, the Dwemer took advantage of the weakened Falmer, and enslaved them. Over time this caused physical and mental deterioration, creating the blind, hunched Falmer seen in Skyrim. The Dwemer were hesitant to share resources with the surviving Falmer, forcing them to eat the strange fungi found in Blackreach. Although allowed to live in Blackreach, the Falmer were not treated as kindly by their kin as they had hoped. After the death of the Snow Prince, the surviving Falmer fled underground, hoping to be taken in as refugees by the Dwemer as fellow Elves. This led to the Battle of the Moesring, where a human child named Finna killed the Snow Price after he cut down her mother, throwing her sword through his chest in grief. Ysgramor's army pursued the Falmer to Solstheim. Falmer attempts to rally were only met with further defeat, leading them to retreat to the island of Solstheim under the leadership of the Falmer Snow Prince. It was these Falmer slaves who built Whiterun and Windhelm.

The Five Hundred Companions killed and enslaved as many Falmer as they could find across all of Skyrim. Ysgramor's revenge didn't stop with military victory. The Elves then met their first major defeat against the Atmorans, with many more to come. He had the help of another Saarthal survivor named Ahzidal who had studied Falmer magic and later became one of Skyrim's Dragon Priests. Ysgramor eventually came back with an army, the Five Hundred Companions. Only Ysgramor and a handful of humans made it out alive, retreating briefly to Atmora and swearing revenge. The expansion of the Atmorans into their homeland startled the Falmer, and Saarthal was razed by the Falmer at some point in the Merethic Era. The new arrivals built the city of Saarthal. The Atmoran migration was led by the Nordic hero Ysgramor. The ancestors of the Nords arrived later from the northern land of Atmora, and began claiming Skyrim as their own. It isn't known when the Falmer first arrived in Skyrim, but presumably, they originated from a group of Aldmer who migrated north after the arrival of the Elves in southern Tamriel. The humans and Falmer of Skyrim lived together on the province's surface in peace for a time, but it wasn't long before war broke out.

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