"So many laws broken, so many people left, just gotta lay low and everything will be fine..."
All Alyssa has to do is survive. Survive and conquer. After all, it's what she has desired her entire life, she has everything required to erase Emma before she becomes her freedom-destorying self. She's given Alyssa one last chance to let everything go and enjoy a normal life, leaving Emma to reign on.
Alyssa agrees, the organisation has given in and ditched her in exchange for their freedom only for their peaceful ways to be met with life ending consequences.
Just blend in, cause no trouble, say nothing, meet no one and stay in plain sight. Any attempt at ending her life, trying again and fading out completely is met with hostile actions and bloodshed.