My take on the end scene from "Cover Story"

As Tony and Ziva lead Landon away, Abby steped forward to hug Gibbs, then she turned towards McGee. Gibbs turned to leave, it looked like they needed privacy, but he only just made it out the door before he hears:

"We need to talk" Abby said seriously
"I'm sorry Abby" McGee began, ready to launch into a full on apology
"Agent McGregor cannot marry Amy at the end. McGee, they are all wrong for each other."

There was a slight pause

"Gibbs I know your there. You do know I'm staying with you tonight right?" Abby shouted towards the door
"You could stay with me?" McGee asked almost pleadingly, he really wanted to make it up to Abbs for almost getting her killed
"Aw Timmy that's so sweet, but Gibbs has bourbon and coffee"
"Come on then let's get you out of here" Gibbs said helping Abby gather her belongings.

Gibbs lead out of the room and towards his car, instinctively putting an arm around her waist. He felt his heart beat just a little faster when he felt her move closer. They were almost at the car when Abby realised she had left her cell phone on the table. Gibbs ever the gentleman went back to get it for her.

Gibbs noticed McGee was sitting on the couch head in hands.

"McGee!" Gibbs shouted
"I'm sorry boss" McGee replied. Although Gibbs wouldn't show it the sadness in his voice wa something Gibbs understood perfectly
"Don't apologise McGee..."
"It's a sign of weakness I know, but it's me that put Abby in harm's way."
"No. It wasn't. You may have written the book but you are NOT responsible for the way that man acted."
"Thanks Boss"
"Now go home" Gibbs added in his usual comanding voice

Gibbs grabbed the item he had come back for and as he was just leaving, again, he heard McGees' softly spoken voice say:

"You look after her Boss"
Gibbs tried and failed to hide the smile that spread accross his face "I always do McGee."

It was the smile on Gibbs' face, the smile that not many got to see, that made McGee wonder just how many times had Abby stayed at his Boss house................