This is a YA book series read in the mid 2000s. One of the last books had a dark cover of a lightning storm over plains.
I believe this story is about 2 siblings, guy and a girl, who start learning magic from a powerful being, hundreds of years old, in a cave.
The goal is to fight an evil, I believe the mentor's sister. They are both very powerful (cosmic power?) beings. She may be called Morgana, not sure.
The main girl eventually falls in love and marries the mentor, and she gains some of his power and a despondent view towards humanity/time (think Dr. Manhattan).
Final battle involves lots of evil monsters, not sure if the good side had an army.