This is around the time of Boxed In. thinking Ziva injured Tony more severely with her bullet ricochet than people realized and he is off on medical leave. In Stuff Happens because that is where the idea hit me right now to have Tony and Emily working together and in a relationship or friendship.
Thunder sounded outside Gibbs House that evening. He was in his basement working on something when footsteps sounded on the stairs. "Still can't sleep during a storm Dinozzo?"
He said "Have something on my mind boss or someone. I really want something to happen with Agent Prentiss. Her boss offered me a job at the BAU when my arm is healed up."
Gibbs looked at him. "Do you want it Tony?"
He said " Yeah I think I do boss. I know Fornell put in a good word for me. It's time, I can't trust Ziva to have my back in the field and I well just need a change."
Gibbs patted his shoulder. "You do what makes you happy. You're a damn good agent and you're ready for whatever the FBI dishes out. Now go get some sleep , if you want I'll tell the team. You have vacation and other time you can use. "
Tony nodded. "Thanks Gibbs. I don't want a big show. I just want them to know I needed to move on. I will tell Director Shepard myself though. She should hear it from me. "
Gibbs nodded. " I'm going to work a bit longer. The fire should keep you warm on the couch. Just add two more logs."
Tony smiled. "On it boss. I appreciate you letting me stay here while the heat is down at my apartment building."
He replied "Your lungs don't do well with the cold , I remember. Make sure you tell your new boss that ."
Tony shrugged. "I will though it should be in my file for them."