Basically, Twilight was still taken under Celestia's wing as her prized pupil, but this time with malicious intent. Celestia was already Daybreaker at this point, and she had banished Luna to the moon after she realized that her elder sister was ruling with crocked ideas. Twilight grows up isolated from basically everypony else, even her real parents, and was taught by Daybreaker that nopony but her is to be trusted, tricking her into valuing knowledge and power. She secures this by using her powers as well as the nightmare forces to turn her into an alicorn at the promise of said knowledge and power, and that they will rule all of Equestia together, something that Daybreaker claimed that Luna failed to do.
Times passes and at some point when traveling to Ponyville to cause some destruction for fun, Twilight spots this pink pony just kind of chilling there and is basically like, "Hey mom, can I keep her?" "Huh? Yeah, sure, whatever."
Though because she soon gets attached to Pinkie Pie, she starts realizing that everything that Daybreaker had taught her was wrong, and with Pinkie and eventually the rest of the main 6's help they bring back Luna, rescuing her from her moon prison, and they defeat Daybreaker together. They also maybe kiss and stuff :3