Endermen Arrival theory

This theory explains the appearance of endermen in the Overworld.

Theory
Before their arrival, the endermen were only found in the End. However, as the End is physically located above the Overworld, some of the more adventurous endermen decided to pass the void under the End. Many of them died, as the void is lethal even to endermen.

However, a few of the endermen survived and successfully entered the Overworld. This drew attention of then-Overworld inhabitants, especially the strongholds builders. Their magicians were inspecting the ender pearls and the end stone carried by the endermen, and finally crafted the end portals. First invaders entered the End.

This angered the endermen, who started their own invastion into the Overworld. Their attact was powerful, and the stronghold builders had to shut down their portals to stop it, before being killed.

Thus, all that remains of once devastating invasion, are the remnants of the endermen forces, and the destroyed fortresses and deactivated portals of now-extinct stronghold builders.