The phone call between Jake and Gibbs in the episode 'Blood Brothers', referenced by Abby and Palmer. I recently re-watched this episode and wanted to know what was said, so this is my thoughts about how that conversation could have gone.
Gibbs picked up the ringing phone on Bishop's desk as he was walking out of the NCIS bull pen for the night. He knew that Bishop was already at her parents' house in Oklahoma, having heard from her a few hours earlier. He had spoken with Vance to make sure that she had time off, and most of the agency knew not to call up to her desk. And, besides, it was almost eleven pm. If there were any cases to work on, the call would go to Gibbs' desk phone or cell phone if it was urgent.
Who would be calling Bishop at this hour at work? he thought to himself before he answered.
"Agent Bishop's desk. Gibbs speaking."
"Agent Gibbs. It's Jake..."
"What do you want Jake?"
"I need to speak to Ellie."
"She isn't here, and you know that."
"She won't answer any of my calls."
"Gee, I wonder why that could be? Jake, you need to listen carefully to what I am about to say to you. What you did to Bishop was cruel. No, it was beyond cruel. It was downright stupid and inconsiderate. She has always been there for you, listened to you, loved you. And you repayed her by cheating. Did you ever stop to think that she might find out? That it might hurt her? You must not have, because if you did, you wouldn't have done it. Bishop told me what you said to her- that you didn't mean to cheat. You lied to her, yet again. She has never been a liar towards you, so what possessed you to lie to her? She's your wife, yet you treat her more like a toy than a person with feelings.
"You want Bishop to talk to you, but you won't give her a chance to process anything that you put her through. When you were overseas and nobody knew if you were alive or dead, Bishop was devastated. She refused to go home or take a break, scared that if she did stop searching for you, she would lose you. She was so relieved to see footage of you on a taxi camera. But then, when everyone else called to let their loved ones know they were okay, you conveniently forgot to call her and let her know that you were okay. She called you so many times, and you never answered. Were you busy with that other woman at the time? I would think that you were, and calling your wife just didn't seem to be a priority right then. You know she convinced herself that you were in trouble with Internal Affairs because it helped her cope better than thinking that you were cheating on her? That's right. She wanted you to be in trouble because it was something that could be dealt with. She didn't want you to be cheating because it hurt her too much to even think that it was a reason behind your actions and secrecy."
"Gibbs..."
"Shut up, Jake. I'm not done. You are damn lucky to have that woman in your life. Bishop cares about you more than anything. But, right now, she's crying so much because you broke her heart. You hurt the poor woman, despite everything she tried to do for you. What is it about this woman that makes you think it's okay to cheat and break your marriage vows?"
"I didn't want to cheat, you have to understand that."
"Do I? If you didn't want to cheat, you wouldn't have. Nobody forced you into it. You did it yourself."
"Okay. Maybe I did. I know what I did was wrong. I want to make amends."
"Bishop doesn't want to speak to you. She doesn't want to see you. And I can't say that I blame her. You broke her heart and lost her trust. I don't know if she's ever going to forgive you for that. And as for speaking to her, I won't make this harder. If you want to talk to her, wait until she's ready to come back to DC. If I find out that you went to Oklahoma, or that you called her again after she asked you to leave her alone, I'll be coming to deal with you. Do you understand that?"
"Yes."
"You better understand, because I'm not just saying this. I really will do it." Gibbs hung up the phone, feeling tension leave his body now that he had spoken to Jake.