Legend has it that if any harm came to a nemeton, the surrounding towns and villages would suffer misfortunes.
In 1943, the nemeton of Beacon Hills was still standing.
When Derek killed Paige on the roots of nemeton in 3x08 - Visionary, he inadverently gave the tree some power through a sacrifice. This power allowed Jennifer Blake to survive her attempted murder and become the darach.
Now that the nemeton has been activated, more supernatural creatures are being drawn to Beacon Hills. The nemeton continues to make an appearance in Stiles's nightmares, and when Derek goes on a vision quest to speak to his mother, she appears to him standing upon the nemeton's stump.
Noshiko Yukimura buried the fly that housed the nogitsune's power in the nemeton's roots. When Scott, Stiles, and Allison sacrificed themselves to the nemeton, the renewed power released the nogitsune.