Another nephilim-situation:

The protagonist decided to live on their own instead of living in an institute because they don't want to live in that strict schedule out of training and missions.

The protagonist ends up saving Alec/Jace/Izzy/Clary and they become friends or even more.

The protagonist can also save a downworlder, if you want to step into the werwolf/vampire/warlock/seelie-topic.