McGee discovers his apartment has been torn apart by a robber trying to locate an item of great value hidden somewhere by the convicted criminal who previously owned the unit while Congresswoman Flemming tries to persuade Director Vance to pursue a career in politics.
The triple-murder case that resulted in DiNozzo getting his (and later McGee's) apartment at a bargain price was expanded on in this episode.
In addition to the infamous triple-murder case noted above, it was also revealed to be the site of another murder taking place 15 years earlier regarding a Praulia heist.
Aside from McGee and Bishop, it was revealed that Nick Torres knew about the apartment's history some time prior to the episode, but Alexandra Quinn and Delilah Felding didn't know until this episode (the latter at the very end).
McGee is revealed to have put his father's ashes underneath the bed until he can find the time to spread them to the winds, with Delilah Felding knowing and supporting the decision. Ironically, the location of his father's ashes was directly above the hiding spot for an actual corpse inside the same room.
It is possible that Leon Vance and Jenna Flemming may have started dating.
Director Vance potentially leaving had been hinted at in A Many Splendored Thing (episode), where Jenna Flemming offered the position of Director to Gibbs in the ending of the episode.
Timothy McGee's apartment being tied to a criminal investigation in the past had previously been alluded to in Return to Sender (episode), where Timothy McGee discovered how then-Special Agent Anthony DiNozzo (the former owner of the apartment) had gotten the apartment.