On her way to work, Ziva sees two motorcyclists, whose faces remain hidden beside her. This reminds her of her old Mossad-assassination days, which shows the viewer a flashback to a similar scenario. She follows them, weaving through the streets. Just as they pass a cafe, an explosion goes off, which causes Ziva to swerve onto the curb. She jumps out of the car and notices a few people dead on the ground (we later find out one is wanted by the Israeli government, and 2 FBI agents who were with him for protection).
One of the attackers walks away, Ziva stops him, and realizes it was her old partner from her Paris-Mossad days. She lets him walk away (One could argue that she is in shock because she didn't expect it to be her old partner, or that her father was behind it).
Ziva immediately goes to the Israeli embassy to try and sort out what happened, claiming they were 'sloppy'. Michael (the guy in charge) claims that Mossad had nothing to do with the attack, Ziva disagrees and that it is for this reason she no longer talks to her father. Michael swears they had no idea, but Ziva says it was her old partner that she let go. Michael further denies this by saying that her and her father attended his funeral. She tries to leave, but is prevented, she isn't even allowed to call NCIS.
Back at NCIS, Abby is nervous and chatty, usually when something is bothering her. We find out she is anxious for the return of new team leader, Tony, who has gone on holiday. She walks to McGee's new desk (Tony's old one) and checks out Tony's flight schedule because he isn't at work at the time he said he would. Soon after she checks Tony's flight details, speak of the devil, Tony walks through the elevator doors; Abby smothers him in her usual Abby-hugs. Tony gathers the team around for gift giving: McGee gets a David Hasselhoff CD, Abby, a gorgeous cross necklace, Ziva, a Swedish girl outfit. He realizes that he hasn't bought anything for Agent Lee (who has joined Tony's team), so he makeshifts a gift, a smuggled in stapler from Germany, but is really from his own desk.
Cut to beautiful Mexico, Gibbs is all 'dirtied' up, with beard and all, fixing Frank's leaking roof. Gibbs is given the phone, and realizes it is Ziva. She believes he is the only one who can save her and as we remember from Hiatus 2, this is her collecting her due.
Back at NCIS, Lee brings up the issue of Ziva being late, Tony dismisses that anything is amiss, but after a while realizes something is up. Director Shepherd tells Tony that they will deal with the FBI, who have come looking for Ziva. (We learn that she is wanted for espionage and murder.) Because of her link with Ari and Mossad, the FBI believe her to have used NCIS as a way to 'get in' in order for her to attack the 2 dead FBI agents.Both Director and Tony don't buy it, but Tony is forced to cooperate with Agent Sacks (Slacks according to Tony).
Downstairs in autopsy, Tony, Ducky, McGee, Abby and Palmer (BlackLung) form a secret alliance to find Ziva w/out Director or FBI finding out. Abby cuts in, saying she has spoken to Ziva already. Tony calls her, Ziva says she'll kill Abby. Tony says hes going to try to help but needs to get in contact with Gibbs; Ziva hands the phone to him, and Gibbs tells Tony he has 10 secs to tell him the details b4 he hangs up.
Ziva and Gibbs go to one of Ari's old safe houses to look for clues. One of the motorcyclists is found sitting on the couch, bullet to the head. They search the house, and find nothing. A mobile starts to ring, Gibbs answers. It is Ziva's old partner, who can see them from a secret camera in the vent. Ziva realizes the call is to keep them there longer so that he can blow it up - they find the camera in time and are able to escape unharmed.
With the evidence, Gibbs is 'temporarily reassigned' and the team are with Abby sorting through what they can work with, while Ziva is in a safe place: Gibbs basement. They find a trace back on the camera to an apartment. Gibbs calls Ziva to tell her what they've found and for her to stay put. She hangs up because she wants to leave to catch the people behind all this. All the while, the Director, FBI and Israeli govt know that this is bad for both countries involved and will ruin all relations.
At the apartment, we find the agents but it is Ziva's old partner and a female. He puts on her necklace and she shoots him, then smothers him, saying that she cant let 'them know that her govt was behind this'.
Ziva enters the room, and the 2 women fight. Ziva is obviously faking that she cant fight, so that she can get some kind of testimony from the agent. Finally Ziva get the confession needed, that she works for the Iranian govt prompting Ziva to kick butt like usual. She ends it by knocking her out. Gibbs, Tony and McGee enter, thinking Ziva has killed both agents when she reveals that she is 'no longer a trained killer, but an investigator' showing the recorder taped to her stomach!