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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 seriousily love this show even though i have only watched season 6,7 and 8 but what i don't understand is why ppl want to see tony and ziva together. From having watched the last 3 seasons i felt like that they have more of a brother sister type relationship.

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i agree with Superman on pretty much everything!!!!!!!!!!! even though she's been in America for a while, Ziva still has MADDDDD skills and she needs to show them wayyy more often. and McGee, hes a special agent for a reason, they need to show what he can do! CI-Ray= NOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO,, he's gotta go, hopefully Eli isn't pulling another "Michael" incident, Ziva will go crazzzzzayyyyy. TIVAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA!!!!!!!!

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I have to start out by saying..I think that abby is the cutest thing on the TV and for Ziva, pleasnt dreams of her at night.
I don't think that a romance between team members would be good for the show,keep it as it is. EJ is a spy and Tony will have to deal with her,but will not be sorry for it.
I do beleive that Gibbs do need to get involed with a nice person as Shadon was,this would be good for the show,and I hope Palmer has a good marriage, also Duckie needs to have more romantic relationship, I'm pretty sure that Duckie will see where the arm was cut open and something remove and brings it up to Gibbs and that Gibbs will know what Tony is working on but will not let it be known until the end. COME ON SEPT 20th

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What with the tongue in cheek reference to Ducky as a young man looking like Ilia Kuriacken, why not bring Robert Vaughn on for an episode or two as
either a bad guy or a friend of Duckies?

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I think Gary Glasburg is a class act! I really like his writing and the way he's running the show. He's a big improvement on Shane Brennan. I love that Gary has given us back the Tony we loved so much from the early days. I hated what Brennan did to the character, turning him into a complete idiot who was only there to suffer putdowns by Ziva and for the others to mock. He wasn't a competent NCIS agent anymore - he was just there for cheap laughs. I feel sorry for Weatherly having to act that awful stuff. I also like that Glasburg has dropped the heavy handed Tiva. A lot of people can't stand it and think it dragged the show down. I'm not keen on McAbby either - I don't think the show needs these silly romances or constant accusations of jealousy. I am really glad GG is talking about a return to the team caring about each other and pulling together and having each others backs. That's been missing for a long time. I hope we see lots more Tony and Gibbs and Tony/Gibbs scenes, and lots more of Abby and Ducky. I'm not a fan of Ziva or Tiva so I'd be happy if there was little of the former and absolutely none of the later. Go Gary!

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Lots of good ideas and fallout I have seen above. My interest is in Tony/Ziva 'sealing the deal' as one put it. I have great faith in the writing and the actors abilites to pull it off which ever way they choose to take it. They obviously have already 'done it once' while undercover. I don't recall where it was however. I HATED to see Franks go. Just wanted to add that this, IMHO, is the best show going right now.

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How about the possibility of Gibbs's daughter Kelly being alive and was protected all this time by Mike Franks. And now who will help her?

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Ducky – This character needs to surprise the Heck out of us all ! There is so much potential to what can be done with him, that it makes it a hard call as to where to go. I’ll think about it, and post, again, later.

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Palmer – This guy needs a very cute, to the point of distraction kind of cute, wife. She can be thrown in around Tony and McGee to trip them up, etc. She might even hold a surprise at how supportive she can be from a different occupation – No super secret spy, or double agent, trying-to-kill-everybody nonsense this time around – Palmer needs a break.

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Vance – While a hard character to get to know and like, he grounds the crew politically and as a head figure to the organization that makes tough choices in D.C. He is the only character with a spouse at home, and children – this might have to become a focal point with his wife being diagnosed with a near-fatal or fatal illness. It’s time to bring a little light into his past, and put him in the field on assignment, or running the team for Gibbs, while Gibbs is otherwise indisposed – show he can walk the walk.

NCIS Quotes

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.

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.