It starts after the first Avengers movie. Loki is brought back and put in his prison cell, like in the beginning of Thor: Dark World. Fandral is his main guard, and he decides that he's going to pretty much do what he wants with Loki, and starts abusing him. Loki is raped every day, denied clothes and most meals, abused horribly. Burned at one point, I'm fairly sure. Fandral also lets other prisoners to rape Loki for his own amusement. I know that at one point during a rape, Loki turned into his Jotunn skin and the prisoner who had been raping him at the time died. There was also a Jotunn prisoner, who had been the only one whose rape hadn't hurt, and Loki had convinced himself it wasn't rape with the Jotunn.
Loki's family has no clue that this is happening. Fandral tells them that Loki refuses to see anyone, that he refuses Frigga's gifts etc. The fam wants to give Loki his space, but there are a few times when they insists. During those vists Fandral gives Loki some clothes and stuff into his cell so it wouldn't look too suspicious. I know one time Thor came by unannounced and walked in on Fandral raping Loki. But Fandral lied and told Thor that Fandral and Loki were just lovers, don't worry about it (basically). Thor buys it. I'm fairly sure Loki doesn't complain or tell anyone because he's afraid of the Chitauri and also believes no one will believe him over Fandral. After the other prisoner is killed, Loki is also worried that if anyone finds out his sentence will be made longer and he'd have to be under Fandral's rule forever.
Eventually, the truth comes out. Thor and Odin are pissed and disgusted and horrified at what had been happening right under their noses. Loki is removed from the cell and into a comfy room (not sure if it's his own or not), but he's in a very bad state. He thinks that the moment Thor and Odin learn that Loki had gone along with his abuse and had caused the death of one prisoner, Loki will be put right back into the cell and back under Fandral's control. So he runs, but before he can get out of Asgard, the Chitauri track him down. Thankfully, Thor and Odin find him and the healing can finally start.
I'd love to read it again, if anyone can point me in the right direction.