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NCIS Season 9 Spoilers: E.J., Kort, Ray, Tony's "Assignment" & Much More

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The Port-to-Port Killer was finally stopped in the NCIS season finale, but the story arc didn't die with him. If anything, "Pyramid" posed more questions than it answered.

The fallout won't end with Mike Franks' swan song or the SECNAV's resignation, that's for certain. But where do the events of last night leave our team going forward?

Between the file handed to Tony, E.J.'s shady actions, rogue agent Trent Kort, and the mysterious CI-Ray and his connection to Ziva, it's hard to even know where to begin.

NCIS executive producer Gary Glasberg, who wrote the episode, discussed it in an interview today, while teasing the upcoming ninth season as well. Excerpts below:

Picking Up the Pieces

On E.J.'s next move: "She’s giving up her post in Spain and most likely taking a leave of absence, if not more than that. We’ll have to see where things end up for her."

On what E.J. removed from Gayne's body: "It’s intentionally mysterious. It’s a little microchip and will absolutely be something that will come into play next season."

On Gibbs leaving the door open for her return: "This show is good at picking up things that haven’t been touched in awhile and revisiting them when appropriate."

On Cobb's surprising surrender: "I wanted it to be very unexpected and to take [the characters] by surprise as well. There’s a nice little moment where they hesitate because they can’t even wrap their heads around the idea that he’s walked in."

"So there’s a built-in pause that happens before they reach for their weapons that was just a nice little touch that the actors decided to do that I was really happy with."

On the idea for Operation Frankenstein: "We knew that Vance was facing some significant issues after 'Enemies Foreign' and 'Enemies Domestic,' and we recognized that his relationship with the Secretary of the Navy is a complicated one."

"This was an opportunity to connect them both to an operation that they were involved with that could explain some of the layers of their relationship."

"Operation Frankenstein was a concept Vance came up with. SECNAV thought it was worth following through on. They attempted the project, and in many ways it was successful. But there was one aspect that even SECNAV lost control of."

"At the end of this episode, SECNAV recognizes the flaws, and that a lot of the weight of what happened falls on his shoulders, thus the analogy to the pyramid. And then the decision ultimately is his to do the right thing and resign."

The Director

On whether Gibbs knows it was Vance's idea: "I would imagine that Gibbs is probably privy to how a lot of this unfolded, and in some ways, that will even the playing field between Vance and Gibbs a little bit as they move into next season."

"My goal is to have the team, as well as Gibbs and Vance, really have to work together as a unit a little more in Season 9."

On bringing the team together in this year's finale: "It was a very conscious decision on our part. We thought going into the ninth season, and because it seems that audiences really respond when the group has to band together, that it would be a nice change to enter a season from that standpoint instead of breaking them up."

On the role of SECNAV next season: "He’s not an adversary, he just has a different approach to things and there’s information that he’s privy to that will drive us through a lot of Season 9. Politics and Washington are gonna play a big part in this next season. It will give us the opportunity to see another side of NCIS that we haven’t focused on as much."

On whether we've met the person Tony is "assigned" to: "Yes. And that story line will probably pick up in the season opener. That’s definitely something that will impact the team. I’m not sure yet how long it will go on, but it will definitely have ramifications that we’ll follow through for awhile."

On Gibbs' basement project: "If you go all the way back to the mid-January episode called 'Recruited,' that’s when we started to see Gibbs start to build something new in the basement. Based on the letter that Gibbs had been holding to from Franks, the suggestion is that that’s the time when Franks wrote to him and told him about his illness, and knowing it was terminal, that’s when Gibbs started to do this for his friend."

On the death of Mike: "It wasn’t an easy decision for us. We love Muse Watson, we love the character, their relationship is very special and unique."

"The interesting thing is, we were very happy with the way that 'Swan Song' came out and the use of Franks as this voice that spoke to Gibbs internally."

"The opportunity is there for that conscience or voice to return again at some point. So I won’t say that is the last time that you’re gonna see Muse Watson."

Gibbs and Franks

On Ray's text reading “Kort in Tel Aviv. Handle ASAP.”: "Well, it’s supposed to leave you thinking, not only about the relationship of Ray Cruz to his fellow CIA agent Kort and what his assignment is, but also the fact that Kort is in Israel and how that relates to Ziva and her father. That’s something we’ll definitely return to, probably not in the Season 9 premiere."

"Again, one of the highlights for me of working on this show is being able to plant new seeds and revisit them as the new season progresses."

On the McAbby moment: "They have a history together and an emotional connection, and I’m anxious to see what the new season might bring for the two of them. We’ll see as we go along and hopefully have some fun."

On Ziva and Ray: "[They are] a little open-ended at the moment. There isn’t any closure to it. We’ll have to see where it leads, but I think he was pretty clear that he has a job to do at the moment, and that’s gonna be the primary focus for him."

On Jimmy's engagement: "I have a feeling that the diehard fans are gonna really enjoy the fact that Palmer is engaged. There has never been an NCIS wedding, and that might be something fun that we can take advantage of later on."

What did you take away from last night's NCIS season finale, and how do you see these events taking shape when the show returns for Season 9? Discuss below!

Steve Marsi is the Managing Editor of TV Fanatic. Follow him on Google+ or email him here.

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I just wanted to say thank you for such a great series. I love the whole cast. I watch the reruns over and over and wait for the new episodes. Again thank you.,

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How do you know ducky is dead? Just because it looked like a heart attack does not mean death

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I'm confused does this mean the show is over? Ducky was one of my favorite charaters. I can't believe what I just watched. Please tell me the show isn't over for good. What happened to the other charaters?

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Oh my god! Ducky died and I dont know if anyone else is dead or alive I hate cliffhangers and I hate not knowing if anyone is still alive!!!!! If either Abby or McGee is dead I will cry for god knows how long.

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WOW!!!! Y did the last season have en with ducky dying? i love ncis but idddkkk now.

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WHY DOES EVERYONE WANT ZIVA AND EJ TO BE TRAITORS!
ok i get EJ but if she wasent with tony she would be awsome if writers of ncis reading but tony and ziva toghther make vance traitor get rid of CI-RAY hook up abby+magee, gibbs+mrs hart the lawyer and ducky+DR gorden

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I love the show NCIS, and the season been great with a couple that JLC been in she brings the show down , using the other characters has helped i believe, i loved The Good Son, Vance did an excellent job, But the JLC character with Gibbs she got to go, she brings the show down

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What happened to the lawyer chick that was the mole? Are we ever gonna find out what was going on there? Who she was getting info for? Heard rumor that tony was gonna be killed in a car crash. Please say this is not true.

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I just got hooked on this!!! Exciting and fun just to watch. I couldn't help but notice Gibbs & Abby have a very unique relationship I'm new to this series but I am totally gonna ship these two. I hope to seem more of them!!!

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Thank god NCIS is finally showing in Europe !
I am loving series 9 and can't wait to see each new episode
Well done to the whole cast for a fantastic job!
cheers

NCIS Quotes

McGee: Rule number 70 - keep digging till you hit bottom.
Abby: McGee! There is no rule 70.
McGee: Well, I--
Abby: You just made up a rule. This McGibbs thing has really gone to your head. I don't even recognize you right now.

McGee: All right. Well you should probably know that Abby and I used to date?
Bishop: Ew. Like, each other?
McGee: Yeah.
Bishop: Wait - isn't that a violation of rule 12, never date a....
McGee: It was a long time ago. After we'd broken up, one night I went to her lab. Found a scribbled piece paper; a list. Potential boyfriends had to fulfill certain conditions by a pre-arranged date or else, goodbye.
Bishop: Such as.
McGee: Things started off relatively normal: opening the door for her, flowers, putting the seat down. Then around number 8, it gets uh...
Bishop: What?
McGee: Does she know you have these?
Bishop: Does she know you have these?
McGee: Yeah she wasn't happy when she found out.
Bishop: These are all very specific.
McGee: Yeah.
Bishop: These ideas apply to you?
McGee: No those rules weren't in place when we were together. At least I don't think so.
Bishop: What's with the two month cutoff? Abby's sabotaging herself. I've seen stuff like this before. We have to talk to her.