Hey so this takes place in between 'Props' and 'Nationals'. I will go to the end of the season and then back track to 'Heart'. To be clear Rory was beaten by his father and mother along with the foster home people and bullies.

"Alright," Mister Shue stands and faces the sea of mostly happy faces, "Rory should be here any minute and needs to say... somethings." No one really respones so he sits with a sigh next to Emma, Bieste, and Sue. Rachel smiles and whispers something to Finn. Sam and Mercedes in the back hold hands and talk about what he might have to say.
"Do you know?"
"No. I wish I did. I guess I kind of owe him for lacking on the whole valentines day thing." Mercedes smiles looking over at Joe.
"Oh I don't know. You were the one to introduce those two." Sam smiles and "Wait what?" Sugar sits on Artie's lap hoping that Rory has good news so she could stay with Artie.
"I think we're fine, Shuoog," Quinn and Kurt talk about how when they found out about Quinn's accident it was different than when Rory was in the hospital. This puts Quinn in an upset mood.
"What happened to me was an accident but people did that to Rory,"
"I still can't get the blood out of my mind. I mean it isn't supposed to be so red." Kurt can't wear red anymore.
"I feel like we could have stopped this. We all saw him get pushed, shoved, bullied and slushied and only one time did someone stopped it. That just made him more of a target. Why would you have someone who is already begin bullied for talking into a glee club so he can be bullied for singing?" Quinn laughed.
"You're just jealous because he can sing high and low." Mike and Tina are helping Brittany console Santana who tried once again to talk to her grandmother.
"She'll come around eventually." Tina says with a weak smile.
"I just want to get out of here. I don't care about what Pixie Boy has to say." She flips her ponytail in frustration. That last part was a little bit of a lie. She did care ever since she found terrifying texts messages on his phone from Sebastian Smythe and a James O'Brien. But she didn't say anything about them to him or anyone. She thought she could get help from her grandmother but the elder wouldn't hear her out. Puck and Blaine talk about how bad Puck feels for yesterday when he pushed Rory of all the jocks around into the lockers.
"Why did that jerk even have to go so far as to say 'For a guy in a singing club you can't be all that bad to do that to your little irish shish kabob,'. I'll beat the shish out of him one day." "He was just trying to push your buttons." "Yeah and it worked. You should of seen the distant pain filled look in Rory's eyes. It was terrifying." Blaine knew the look. He had seen it before they all had though no one asked him about it. It is a look that dead unfocused eyes gave and always misting over the sky blue pupils. "Rory's fine. I think the push was just didn't want to make him spill his guts." "I guess what is going to tell us anyway." Joe was waiting by the door, filled with a mix of emotions. He could hardly wait to see Rory but he knew the news was not good but far from it. He stops pacing and looks up at those piercing sad blue eyes. Rory walks in slowly. He looks tired like he had been fighting with himself to find the courage he needed. The whole group falls silent. Behind him, Agents Reid and Prentiss come in silently and stand in the back. Rory glances at Joe and gives him a small smile. Joe smiles back and steps off to the side, sitting up on the piano. Blaine holds his breath not knowing how Rory was going to do this.

"Okay, so there's something you guys should know. Well... okay there's a lot you should know." He takes a breath.
"I've lied to you, all of you."
"Yeah, we get it, Great Gazoo Kid. You lied to Britt to get in her pants." Santana snaps the tension. Rory flinches and closes his eyes.
"Yes that lie and others. Some of you know already." He looks at Blaine.
"I'm gay." Silence fills the room. He looks at Artie and Sugar.
"I'm sorry, Artie. I should of backed off when I found out you liked Sugar. I've known for awhile and I just didn't want to make the jocks right," The room fills with unspoken questions.
"Rory..." Spencer Reid calls for him "the video and the..." he trails off. Rory takes a shaking breath.
"There is more than just the lies. I need... I need to..." Tears start to escape. Fear is mixed with the silence. They have only seen Rory cry once and that came with blood. Santana fills with guilt, even when she saw Sebastian on top of Rory with his wrists pin above him he just walked off with that look.
"Go ahead Rory," Mister Shue says encouragingly, knowing full well what it is he needs to show. He turns his back to the crowd of very confused people. Tears fall and his shaking hands undo the first three buttons before the sob comes. When the tears started Joe got off the piano but stayed by its side. When Rory's tears fell He turns his back to the crowd of very confused people. Tears fall and his shaking hands undo the first three buttons before the sob comes. When the tears started Joe got off the piano but stayed by its side. When Rory's tears fall faster he goes on instincts that he has fought before. He turns Rory to face him and wraps his arm around his shoulders and the other around his back. He jumps like always but relaxes. Rory hands undo the rest of the buttons on his green and blue flannel shirt and he breaks the embrace. The buttons are undone but he hugs his shirt around him. His eyes stare down, tears roll down his pale skin, and his frame shakes.
"There are things about my life that I have never told anyone, ever. Let alone show. Please just don't freak out." He looks at everyone then right into Joe's warm hazel eyes. He steps back and removes the shirt, slowly. The first thing they see is the fresh cigarette burn on the side of his neck. Tears still fall as they see more scattered over his arms, shoulders, chest and torso. Jagged scars covered his chest and stomach as well as fresh ones given to him a few weeks ago. He is skinnier than they thought before and bruises speckle his pale skin. His arms are lined with red gashes. Those who sat before him faces widened at the sight they never considered from the quiet Irish lad this. Sugar buried her face in Artie's shoulder. Rachel's hand met her mouth and Finn holds her. Sam stares and tightens his grip on Mercedes's hand. She squeezes back. Tina starts to cry and Mike holds her. Santana stares and Britt wraps an arm around her shoulder and puts Santana's head on her shoulder. Puck leans forward. Blaine opens his dry mouth but his voice is caught on the sight. Kurt squeaks. Quinn's vision blurs slightly. Biting his lower lip he looks at Joe, fearing his reaction the most. He looks at the ground and shakes his head slowly. Tears still pour out. Joe is stunned but then wraps his arms around Rory's bare skin. His hands feel the scars on the other boy's back. Rory buries his face in Joe's chest, his legs giving out a little. The glee children seem to be frozen in time. Beast, Sue, Will and Emma stand still surprised as well. They knew he had been abused but they never thought it was this bad. Even Reid and Prentiss are shocked.