• No-one really knows how far things got when Gibbs was gone, but from time to time Tony has been heard to call Director Shepard by her first name, something which Gibbs seems to object to ("Just how close did you two get while I was away?"). So the question is was there really something?
• When Jenny goes to the team for some information on the case (Family Secrets) Tony is the last one to give in. This shows that he is unwilling to side-step Gibbs, even if it is the director.

• Jenny, the last director of NCIS had Tony do undercover work for her and her alone. She ordered Tony to date an enemies' daughter so that Jenny could finally get revenge for her father's murder. Gibbs and the crew were unaware of this and there were mixed feelings on Tony's secrecy about his movements.

• They sometimes seem to have a very good relationship, which may or may not extend (or have extended) beyond a professional capacity. Perhaps the relationship is more that of a familiarity between partners than any romantic link, but there are clues that something may have happened. Tony walking in on Jenny whilst Cynthia adjusts her bra. Neither Jenny or Tony are worried by this, indicating there has been a degree of intimacy.
• Alas, we will never know as Jenny was killed in the season finale.

• Gibbs: Tony, where are we?
• Tony: McGee and Abby are working firearms analysis and matching(looks over paper at Jenny) tire marks to vehicles…
• Jenny: (looks at Gibbs)

Kill Ari Part I

• Tony: (stares trying to find somthing to say)
• Jenny: Yes. I really am the new NCIS Director.
• Tony: (smiles)
• Jenny (smiles back)
• Tony: (gets slapped upside the head)

Kill Ari Part II