Story related and cannot be missed. You will unlock this trophy right at the beginning of Chapter 3.
The boss for chapter 2 is very easy. Once you're on top of the flower, the battle will start. From the start ignore the main baddie and attack the tentacles coming out of the middle of the flower. Once all are damaged the Rainbow Butterfly will split up into 7 smaller butterflies. You must attack them in order of the rainbow: Red, Orange, Yellow, Green, Blue, Indigo, and Violet. After that it will be defeated.