Here's the full story as I understand it:
Long ago, there was a demon uprising and the witches and church banded together to defeat the demons. Most notably, the witch of thorns became a legendary figure thanks to her contributions. Things seemed well for a time but there was a famine and the church blamed the witches and their rituals for it. The church began hunting down witches and executing them.
Aradia is a young witch who lived with her father and sister in a village protected by a magical barrier. But the church destroyed the barrier and attacked the village. Aradia's father, now too old to fight properly, attempts to hold them off and tells Aradia's sister to hide her. Aradia's sister finds Aradia a hiding spot and gives her a dagger before rejoining her father to help him fend off the invaders. The invaders kill Aradia's family while she watches in horror. She is also discovered and assaulted/raped.
Eventually, Vendetta finds Aradia and raises her and trains her in combat. At the start of the game, Aradia goes to a bandit hideout to test her skills as well as rescue the women held prisoner there. Realizing that she is now ready, Aradia returns to Vendetta and reaffirms her desire for revenge against the church. The church Vendetta is in is hidden now and Aradia pleads with Vendetta to go into hiding but she refuses, though offers to help you out on your journey.
Aradia sets off on her journey and encounters Suzune, who is a foreigner in search of her brother, who killed her father and clanmates. Suzune is eventually captured by her brother and slavers and becomes a sex slave before being rescued by Aradia. Suzune's journey is, in theory, one of the things that affects Aradia's choice at the end (I'll explain later) but the crux of it is, the pair realize Suzune's quest for revenge only led to her suffering. She departs and has a hopefully happy ending.
Aradia continues on her journey and (going slightly back before Suzune's finale), enters the white cathedral, where another demon uprising has occured. She befriends several survivors (though these survivors all have horrible endings in future diaries) but encounters Candore, who has been sent on behalf of the church to quash the demon uprising. Aradia defeats Candore but spares her life, though she is eventually captured and raped by other survivors due to her defeat.
Finally, Aradia enters the church and sees that the witch of thorns has returned and she has killed the church leaders including the pope. The witch of thorns reveals herself to be the true Aradia and explains to you that you are a clone made by Vendetta. She proves this by revealing that she has the dagger that her sister gave her.
The true Aradia offers for you to join her in revenge. If you choose to join her, you get the "bad ending," where both Aradias continue their slaughter of church members, leaving a mountain of corpses in their wake.
If you choose not to join her, you two fight it out and if you win, Vendetta shows up and you have another choice. (Tbh I only picked one of the endings I don't know what happens if you pick the other option). In this true ending, your Aradia reflects on her journey up til now and realizes that the cycle of revenge will always continue as long as you harbor such a deep hatred in your heart. Had you not seen the consequences of revenge for yourself, such as Suzune's story, you might very well have turned out like the true Aradia. So you kill the true Aradia and commit suicide, thereby ending the cycle of revenge.
Revenge is a major theme throughout this game. There is a theory someone posted earlier that I think is probably true and well thought out. The theory says that every game over you have is canon.
The "idea clusters" are actually "memories." You are collecting the memories of those who have fallen. When you die, Vendetta creates a new Aradia who collects your memories and experiences. This is why, despite having clear endings where your Aradia is dead/enslaved, you can continue your journey with the message "revenge never ends," because your new Aradia will take up your legacy. (Yes, there are some continuity issues with this but it's still a good theory).
The true ending also requires 130 karma to unlock. This means you have to rescue victims and, more than likely, complete Suzune's story to unlock it. This requirement might seem annoying, but it shows how your Aradia and the true Aradia had different journeys. While your Aradia got to see how the revenge of the demons, the revenge of the churches upon the witches, and Suzune's revenge, only continued the cycle of suffering and hatred, the true Aradia only stayed on the path of revenge.
Anyways that's pretty much it. Yeah I nerded out on this one. This is probably the best H game I've ever played in terms of story and animations. Props to the developer.
Some interesting tidbits and notes:
I'm still not 100% sure what Vendetta's role is (thanks translations) outside of creating Aradia. She seems to be on her own revenge journey too.
There are a few game overs where Vendetta is violated, further adding to the revenge theory/theme. In one particular one, Aradia is tortured and interrogated for the church's whereabouts. She eventually gives in and Vendetta is captured as well.
Pretty much all the NPCs you meet have a horrible ending outside of Suzune. The scared nun at the bottom floor of the cathedral ends up raped. The two nun girls you help out are captured and raped in front of each other. One of the particularly sad ones for me is the inspector girl you meet near the midpoint of the game. She and her men encounter tentacles and most of her men are slaughtered. The survivors mutiny on her, thinking it'd be better to use her body since they're all going to die anyways.
