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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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    Hey does anyone know when the new season starts? And who is all coming back???

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    i love watching ncis they all make a great team and you can have a laugh at ziva when she gets her words mixed up,they complement each other - and it just gets better and better-please never stop

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    Of all the US crime series, NICS is by far my favourite. Gibbs' team, from Kate to Ziva, are marvellous and the stories and plots are consistently strong and credible. I love the humour and my crush on Mark Harmon is always notched up when he smiles that wonderful smile. This is a super programme. Thank you to everyone who is connected with it and long may we continue to enjoy it in the UK. Its strength is reinforced by the number of times one can watch repeats and never be tired of them.

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    I really enjoy watching NCIS i have been watching it since the first season. i love the characters and i hope no one els dies.

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    because i love this show so mutch.
    is dr malerd ok / ducky i hop he did ot die he is what ,makes the show as whell as gibes and the rest of the crow.
    zeva is my persoal favorite she is so good at taken down the bad gys.

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    when is the new season of ncis ginto start

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    I love NCIS. I watch all the reruns as well as the new weekly shows but I WILL BE VERY DISAPPOINTED IF SOMEELSE DIES ON NCIS. I LOVE THE CAST....EACH ONE CONTRIBUTES SOMETHING TO EACH SHOW. PLEASE, PLEASE DO NOT KILL OFF ANY OF THE CAST. I HATED THAT KATE AND JENNIE DIED BUT WHEN MIKE FRANKS DIED, IT TOOK SOMETHING FROM THE SHOW. MY QUESTION WOULD BE "IS THIS WHAT WE WILL EXPECT AT THE END OF EACH SEASON, SOMEONE DIES"? I HOPE I SPEAK FOR ALL THE THOUSANDS OF FANS OF NCIS WHEN I SAY "PLEASE DO NOT KILL OFF ANY OF THE CAST"