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.)
Chapters (1)
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That's mean of harmony. :(
Pffffff
that definitely got a chuckle out of me
Look, the poor thing has only so much experience with linear time, much less organic life. This went far outside its usual bounds and expectations. Really, it's on Sunset for making so many assumptions... though if she ever does encounter the Tree's avatar again, she's more than entitled to punch it in the muzzle.
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Sunset was never said to be that smart at this age to be fair.