Taya's backstory. Both her parents were murdered by thieves, resulting in her becoming an orphan roaming the streets of Catro, until Nav discovers her and takes her back with him.
Celestia's breakdown when she sees what Nav has become partly as a result of her actions, and her lamenting how much she hates her crown.
Most of the stuff that happens to Nav after Discord brings him to Equestria in the first place.
Nav getting the chance to say his final goodbye to his twin sister when he goes back in time.