Rebecca escaped the PIT, found a family among the Freeman...and watched too many loved ones die. All she wants is the Cardinal to leave her in peace, but he's made it clear that's never going to happen.
When the Cardinal attacks other Freeman villages, she finally understands that no one is safe from his wrath. As the only one who's stood up to the evil that is the Cardinal, it's up to her to convince the others that they can't hide forever. It's time to fight.
The Machine predicted Rebecca would become the Cardinal's enemy. It may have gotten that one right.
In the conclusion to the Acceptance series, enemies become allies and old friends emerge, but in the end, sacrifice may be the price of freedom.