The Hylian Civil War was a brutal battle for the Triforce; Hylians versus Hylians, Gorons versus Zoras, and so on and so forth. So much death and so much bloodshed, but in the middle of all that was one of the darkest places in Hyrule history; Kakariko Prison. This wasn't like any normal jail, because this jail was corrupt.
It held prisoners of war, which alone, is disturbing. They would interrogate the prisoners the find out everything they now about Kakariko Village's adversaries. If they told them everything, then they were either freed or turned into a slave. However, if they didn't tell anything, they were tortured until they talked.
The type of torture depended on the mood of the prison's warren. Sometimes the prisoners were beaten with a whip, other times they had their hands cut off. If they still didn't talk, they were executed. Some were decapitated; others were hanged by their feet and beaten to death. There were also the unlucky ones who were thrown into the acid pit that was in the basement, but the most disturbing was when they started burying people alive in the field in front of Kakariko Prison.
Then after months of fighting their way through the war, a team of Hylian Royal Knights invaded Kakariko Village and raided the prison in hopes of saving some prisoners, but unfortunately they were too late. The prison warren and the guards fled days before the raid and all that was left was Just puddles of blood and dead bodies. Being the sympathetic people they were, the knights buried the dead bodies in the prison field and had a priest come and bless the graves of the prisoners. Years after the war had ended; the field in front of prison had become a cemetery for the locals of Kakariko Village and Hyrule Castle Town. The Prison had become boarded off and covered in the darkness. This gave it the nickname The Shadow Temple.