One night, the Tree of Harmony disguises itself as an alicorn to appear in the basement of Celestia's School for Gifted Unicorns.

A few days later, Sunset Shimmer and Princess Celestia heatedly discuss a night of passion only one of them knows anything about.

In the MLP:FiM episode "What Lies Beneath," the Tree of Harmony took the form of Twilight Sparkle, trapped the Student Six in caverns beneath the School of Friendship, and put its captives through weird ordeals to test them, threatening to hold them prisoner for longer (maybe forever?) if they failed.

In what world does that NOT make the Tree at least a part-time villain?

(This story might be an entry in a "Sunset x Former Relationships" contest.)