If she survives and is persecuted by everyone she's ever known, then maybe she asks you if you know where the ones she remembers are important to her are. You take her to see the Gurus, starting with Melchior, then Belthasar, and finally Gaspar at The End of Time. They offer her their final bouts of wisdom, and choose to either let her stay at The End of Time or send her back to the Dark Ages to be judged- and most likely executed- by the people who remain. If you let her stay, the two of them tell the party goodbye. When they're alone, Gaspar tips his hat to the Queen and leaves, going into that blackness beyond the little station they're at, and so Queen Zeal is left to watch the End of Time just as Gaspar had.