Twilight has the power to change the biological structure of anypony, or anydragon into something else. And, after seeing Rarity fall over other stallions, Spike the dragon wants Twilight to change him into a pony so that he could finally have a chance to be with the mare of his dreams. She gives in and casts a spell on Spike, turning him into a pony. However, this spell is temporary, unless Spike gets his cutie mark within three days.
But becoming a pony for the sake of Rarity comes at a price; Twilight Sparkle will lose her one and only number one assistant, something that is dear to both her and Spike.