It's a sacred space where Druids do their rituals. There are several of them...the one in Beacon Hills was kind of a magnet to the supernatural. It was a tree stump with dozens of large roots underground. This druid we know used it to help me, Scott, and Stiles do this sacrifice where we were spiritual surrogates and for a couple minutes so that we could find where our parents were being hidden, and...I guess it gave the Nemeton enough power to become a literal beacon again. Deaton told us it would leave a permanent darkness around our hearts.
At first it was nightmares, then hallucinations. They've both gotten worse. I tried medication to help me sleep, but it doesn't do anything.