Ootori Madoka falls into the hands of The Universe of the Four Gods along with her friend Himuro Masaki, same as how Miaka and Yui entered. While Masaki goes missing, Madoka is fortunate enough and ends up in the emperor's palace, safe. The story of the series continues allthroughout, following the milestones unless the player chooses different options. Depending of the player choices, some characters who didn't survive in the original series can be saved.

[Edited from Fushigi Yuugi Wiki]