Sheldon returned from his sabbatical to find things different. Leonard was fired from his job at the university and is now drinking a lot. Amy ended their relationship agreement and started dating Stuart. So most nights he was alone by himself.
Two weeks later, Sheldon was working at his computer when Leonard came home reeking of booze.
"Drunk again I see. I don't know what you did to get fired but it's not the end of the world. You could find another university to work at. No need to be constantly drunk."
"Maybe I just want to be drunk. What's it to you anyways. You came back and you think everything should be back to normal. It's not. I'm sick of your bullshit. I'm moving out. I can go live with Penny. I have had to put up with your shit for years."
"Fine. Sign here. You have 30 days. After 30 days if your stuff is still here, you will find it next to the dumpster outside."
Later Sheldon hears Penny arguing with Leonard like never before. They were shouting and cussing at each other. He heard Leonard leave and decided to go over and check on Penny.
Knock knock knock "Penny." Knock knock knock "Penny." Knock knock knock "Penny.'
Sheldon barely hears Penny tell him to come in. Sheldon is now even more worried and walks in and sees a bloody Penny. She has a black eye. A bloody lip and nose.
"I'm going to kill that bastard. How dare he hit you."
"Please Sheldon, don't. It will only make things worse. You will be in jail."
"How long has this been going on?"
"It started a little after you left. It didn't get worse until just recently after he was fired and started drinking more. It was my fault. I didn't have dinner ready in time when he came home. He got so mad."
"That is no excuse for this. We need to call the police."
"Please Sheldon. I can't call the police. It would be so embarrassing. I would lose all my friends. They wouldn't understand. This is only what you see. He did worse. I can't tell anybody else. Can you please just help me get to the hospital. I think my nose is broken."
"I need to call Howard and Raj. I will not tell them why but I need there help. I had already given that asshole 30 days. Now fuck that. I'm throwing all his shit out on the street. I will have Bernadette also come over. You could use her help. She will get you to the hospital while I take care of things here. I will be there shortly. I promise."
Sheldon walks back to his apartment to call Howard.
"Howard, I need your help. Can you and Raj come over as soon as possible? I am kicking Leonard out of the apartment and I need help throwing his stuff out on the street. Great. Thanks. See you when you get here. Also can you put Bernadette on the phone? Hi. Thanks for asking. Can you go in the other room so Howard doesn't hear? I also need your help. Leonard has been abusing Penny. She won't let me call the police. Hef face is a mess and I think that son of a bitch raped her. I need you to help her to the hospital. Thanks. See you when you get here.
Bernadette arrives by herself and tells Sheldon that the guys will be by later. That he needs to go with Penny to the hospital. They head for the er and are seen by a doctor. Penny informs the doctor all that happened and the doctor calls the police.
Detectives Benson and Stabler arrive. Take her and Sheldon's statements. They gather the rape kit evidence and then head out to arrest Leonard.
The next day the guys throw all of Leonard's stuff out on the street next to the dumpster. Sheldon helps Penny move out of her apartment and into his since she can no longer afford her's. She starts seeing a therapist. A month later she has a miscarriage from the rape.
A year later things are finally slowly better for Penny. She has a new job. She still is roommates with Sheldon, no agreement signed. She's going twice a week to the therapist. Leonard is serving time in prison for abuse and rape.
Penny is in the apartment cooking dinner, Sheldon's favorite, spaghetti with hot dogs cut up in it. It's a special occasion.
"Hi Sheldon. Welcome home. I hope you don't mind that I cooked."
"That's fine Penny. It smells good."
Sheldon sits down and they start eating. "What's the occasion? I haven't seen you this happy in 2 years."
"I went to the doctor today."
"Anything wrong? Are you okay?"
"I'm fine Moonpie. She told me that I would be eating for 2 for the next seven months."
Sheldon for the first time in his entire life is speechless. He is so happy he is crying.
"That is wonderful. That is the best news I have ever gotten."
After Penny gives birth they name the girl after Sheldon's grandmother who had passed away the month before. Things couldn't be any better for the three.