[Warning: Spoilers ahead]

Are we to believe that Special Agent Leroy Jethro Gibbs (Mark Harmon) is dead? "NCIS" wrapped up Season 12 on Tuesday night with the shooting of Gibbs in a marketplace in Iraq. First he was shot in the leg by one of the young American men recruited to be terrorists by The Calling, so it didn't look too serious. But then, he took a second shot to the body, which could be fatal.

The shooter was Luke (Daniel Zolghadri), the teen who had stayed at Gibbs' home after The Calling killed both of his parents. And it seemed as if the two were making a connection. The one person who questioned Luke's motives was Joanna (Mimi Rogers), the late agent Ned Dornegett's (Matt Jones) mother, who cautioned Gibbs that Luke was playing him. Boy was she ever right!

"The whole idea of this storyline is that Gibbs and the team find the fact that children are being used in these attacks very unsettling," executive producer/showrunner Gary Glasberg told FOX411 in a conversation following the airing of the finale. "It changes everything that he has focused on over the years and worked towards -- trusting women and children first. Then in this instance, he doesn't know who to trust. This is difficult for him. He wants to help this boy but at the end of the day, this young man ends up being troubled to the extent that it backfires on him."

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It was obvious that Gibbs was very disturbed about the case, so much so that he began seeing dead people when Dornegett's body arrived in Washington, D.C. On the tarmac when the body was being unloaded, Gibbs saw the ghosts of Kate (Sasha Alexander), Jenny (Lauren Holly), and Mike Franks (Muse Watkins), the latter returning for the finale.

"The incarnation of Mike is very much as Gibbbs' conscience," Glasberg says. "That is really what he is doing here. He is saying to Gibbs, 'The world has changed. The landscape has changed. How much longer can you keep doing this? How much longer can you figure out who's good and who's bad, who's right and who's wrong?' With every year that goes by, Gibbs is losing agents. In a post-9/11 world, it keeps changing and it is taking its toll. In essence, Mike is Gibbs' own thoughts, and Gibbs looking at himself and saying, 'Can I keep doing this?'"

In addition to the "Peter Pan" aspect of the story with episodes being named "The Lost Boys" and "Neverland," there is also a touch of "Oliver Twist," with The Calling leader Daniel Budd (Giles Matthey) being a bit like Fagin in his design. But the reality of the story is actually scarier, according to Glasberg, as the idea for this arc came from real-life news stories broadcasting that terrorist organizations are recruiting on the Internet.

It will be the first episode of Season 13 this fall until we find out whether or not Gibbs survives, but what Glasberg did reveal is that since DiNozzo was in contact with Daniel -- the two were on the phone when the attack on Gibbs' took place, "he will take the lead on that aspect of the case and we will see Tony DiNozzo in action. As the rest progresses, the rest of the team will work together as they do as a family and take on The Calling."

So what's up next on "NCIS"? We asked Glasberg for a few hints.

FOX411: What can you tease about the first episode when we come back?

Glasberg: We will pick up right where we left off for the season opener. We will wrap that storyline up early on. As I have done historically, I will probably get into six or seven episodes of more traditional storytelling and into the background of our characters and whatnot, and then figure out what's next and launch something significant. As you know, I like to surprise people a little. As we get closer to November, we will pull the rug out from under people and try something different.

FOX411: This will be at least a 4-episode arc by the time we return next season to find out if Gibbs survives or not. "NCIS" has pretty much been episodic. Why the continuing story?

Glasberg: We are not serializing per se over the entire season, but the opportunity to take these characters that we connect with and that we feel strongly about and let people go on a little voyage with them over three or four episodes is fun. It gives the writers new opportunity, but we will continue to solve crimes episodically and do the traditional episodes that people look forward to. This was just an opportunity to do something a little different. We will probably do some more of it in the future as well.

FOX411: So what's with the leads of both "NCIS" and "NCIS: New Orleans" getting shot? Does what is happening on other shows affect you? Is that the temperature of TV that there has to be more danger for the leading characters?

Glasberg: No. This was a very conscious decision. Last season, we didn't have a cliffhanger. This season I wanted to do something more significant. It was really a decision to do something big and significant with both characters and do some action. Then, we will reset at the beginning of next season. Just raising the stakes a bit. It is not so much what other people are doing or what the climate of TV is. It's just taking it to a different place.

"NCIS" airs Tuesday nights on CBS.

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