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Twilight's appeal to Nabu is surprisingly rational, even considering that she's saying that him taking over would make him unbalanced. The fact is that she's speaking from experience. Twilight was Celestia's best pupil, the strongest unicorn in all of Canterlot. However, it was only once she found friends that she could have the strength to face her greatest fears and become a better pony. Her friends brought order and balance to her life, and if friendship balances, then Nabu recognized the potential truth of her words.