The Well of Souls was a magical device designed and created as a secret project of the gnomes.
The theory behind the Well is explained as extracting the soul of a recently-deceased individual, recreating their mortal body and recycling their soul back inside of that body, thus defying Fate itself.
In Kingdoms of Amalur: Reckoning, the Well resurrects the player's character and is the location where they begin their adventure in Amalur. The character, revived as the Fateless One, is the project's first and only success. After waking in a pile of corpses, the Fateless One is forced to escape from the Well of Souls as it is attacked by the Tuatha Deohn, the immortal blight currently plaguing Amalur in the Crystal War. The Tuatha Deohn do not wish the mortal races to gain the power of cheating death, so they plant magical explosives to destroy the Well. Fomorous Hugues, the leader of the project, distracts the attacking Tuatha long enough to allow the project's only success to escape into The Faelands.