I don't fully understand the story myself due to the translations but from my understanding:
So at the start of the game, you find out you're a witch named Aradia, seeking revenge on the church. When Aradia was a child, the church had invaded her village. Her father and sister hid her away before engaging the church in combat but were subsequently killed. Aradia was discovered in her hiding place and was raped multiple times (as seen in the event with the fat man). She is eventually taken in by Vendetta and hones her skills so she may one day take revenge on the church.
Eventually the day comes and Aradia sets off on her quest; first visiting a bandit village to test her skills and rescue the women kidnapped there. She returns to Vendetta and reaffirms her vow to seek revenge. During this time, it appears that demons have appeared and are clashing with the church in various places including the cathedral. As Aradia journeys, she meets a girl named Suzunne, who is seeking vengeance on her brother, who had killed their father (and possibly others). At the cathedral, Aradia befriends or helps several nuns and other survivors, though to my knowledge the survivors are raped in various diaries. She eventually runs into Candore (err did I spell that right), who had been sent to quash the demon uprising. Aradia defeats Candore but spares her and Candore is eventually raped by other survivors.
Aradia eventually finds Suzunne again, who has been captured and is being kept as a sex slave by her brother and other slavers. Aradia defeats Suzunne's brother and the two see the consequences of living for revenge. Suzunne arguably is the only one with a happy ending.
Aradia continues her journey and she eventually encounters the witch of thorns, who kills the other church leaders including the pope. The witch of thorns reveals herself to be the real Aradia; you were a clone created by Vendetta. The real Aradia offers you a choice: to join her on her quest for revenge or to oppose her. In the join ending, you and Aradia set off and continue killing, leaving a mountain of corpses in your wake and embracing "evil." In the "true" ending, you battle the true Aradia and defeat her. Realizing that you are only contributing to the cycle of hatred caused by revenge, your Aradia kills the true Aradia and commits suicide, thereby ending the cycle of revenge.