Written for the prompt NCIS, Jenny/Tony, Keeping secrets
Their relationship had begun when Gibbs was away, when they had first been ironing out the details of his undercover assignment. Neither of them had planned on it really, and both were aware that it was best to keep it a secret. He had been the head of the major case response team at the time and she the head of a Federal Agency, she was technically his direct superior, it was definitely something they couldn't broadcast.
Keeping secrets and sneaking about wasn't what he had really wanted, but he was doing it with Jeanne anyway, what was one more secret. It did seem hinky, as Abby would say, to him that his lover was practically ordering him to sleep with another woman, but he did it anyway. When everything with Jeanne came out in the open they were the only secret to remain.
Tony had thought that it would have been harder to keep their relationship from Gibbs, but the man was still not completely right after his amnesia. Their relationship was interesting, they still kept separate homes and lives, but they were certainly more than friends with benefits, even if Jenny did seem to be keeping more secrets from him. He supposed that was only right though, there had to be plenty that she knew that she couldn't tell him, he certainly didn't have the level of clearance she had.
Accompanying her to Decker's funeral he hadn't expected anything out of the norm, and when she had ordered him and Ziva to relax for a bit he hadn't been in the least suspicious. When he and Ziva arrived at the diner later, finding out that they were too late he almost froze completely. None of the secrets that she was hiding could have led to this could they, they must have done, but he couldn't believe it. Jenny was dead, and he was partly responsible, they should never have let her go off without them, they should have been quicker to get to the diner, maybe they could have done something to help.
Tony didn't even protest his assignment as Agent Afloat as much as expected when Vance gave it to him. In a way he was expecting to be punished for letting Jenny die on his watch, he wanted to be punished. He had gone to the funeral and stood with all the other mourners, but couldn't mourn as he wanted to. As far as everyone was concerned he was just one of her agents, one that those who knew she hadn't died in a fire knew hadn't been quick enough. He wasn't her lover, they would never know, maybe a period on a ship on which no-one knew him would do him good. He could grieve in private as he wasn't about to tell anyone about their relationship. Jenny had taken it to the grave with her, he would do the same. It was their secret to keep.