So basically, Tony has a case and it's messed up with files or some sht, and then the fbi comes to investigate, and you two find out the other works there (NCIS & fbi respectively) and so then you end up figuring out that they're trying to frame Tony (idk who) and work against the fbi with Gibbs to try and clear his name and you get kicked out of the fbi as a result but still succeed and then get hired on the mcrt when Kate transfers and Tony proposes last chapter
Case Tony is working: Captain Grey (Lt. Commander Randolph's... master? Idk, whatever the word for who she has an affair with) killed her after she went to break it off, wanting to try and fix her marriage.
They had a verbal row, and when she ran off he knocked her out before she could leave and suffocated her with a pillow (hence the absence of bruising around her neck) and no signs pointing to a struggle, only the bruise/cut on her head.