After Mike Franks' "Swan Song" made for one of the best episodes in NCIS history, last night's finale felt less like the season's climax and more like the denouement.

"Pyramid" connected the dots and filled in the blanks involving operation Frankenstein, while dangling a number of intriguing threads that will carry into next fall.

The Port-to-Port Killer, Lt. Jonas Cobb, wreaked plenty of additional havoc on the team before he met his maker, but ultimately went down fairly easily in a shootout.

The more interesting and unexpected developments didn't fully unravel until later. This being NCIS, Cobb's demise was just part of a complex, tangled web.

There were several significant reveals this week, not the least of which being that E.J. Barrett is the niece of Secretary of the Navy Davenport. Naturally, Gibbs knew.

He never spoke of the obvious nepotism that buried him in the P2P case, possibly because you don't just call out SecNav, and it's not Barrett's fault who her family is.

If that were E.J.'s only secret, maybe we'd actually like her after this episode.

Her "moment alone" with the body was chilling (no pun intended) and beyond shady. What was in Gayne's wrist, why was it there and how did Barrett know about it?

You can expect this surprising twist to be fleshed out next season and you can guarantee there are more layers to E.J. than we're currently aware of (although Tony may be privy to more information than anyone else, which we'll get to briefly).

Vance's role in all this was equally startling.

The Director actually conceptualized Frankenstein ages ago, only to watch it blossom into a joint CIA/NCIS operation that went horribly wrong on so multiple levels.

Vance's hands had blood on them, and were tied by the chain of command. There was plenty of blame to go around between Vance, Kort and SecNav Davenport.

With Cobb "evolving" as Ducky put it, his focus shifted to destroying those who made him a creature. That put NCIS and the CIA squarely in the killer's crosshairs.

The weight always falls on the bottom of the pyramid.

In this case, it's hard to tell where upon the pyramid Vance sits, stifled by higher-ups, with his agents at risk, yet due to an operation - at least in part - of his own creation.

When he brutally kidnapped Ziva and then surrendered shortly thereafter, you knew there was more to it. His target wasn't Ziva at all; she was merely a distraction.

Having occupied Leroy Jethro Gibbs and his team, Cobb broke free within NCIS' confines - a bit dubious that he wasn't more tightly guarded - and returned "home." 

With Mr. Palmer, Kort and Barrett held hostage, Vance, Gibbs and SecNav all descended on Frankenstein in what promised to be an epic showdown. It was not.

Davenport, Vance and Kort were all there, and Cobb wasn't making it out alive. Why he didn't he take them out, or at least try? Did his humanity surface, however fleetingly?

In any case, he hesitated and when he drew his gun, the aforementioned trio shot him countless times. Game over. Anticlimactic in a sense, but the demise of Lt. Cobb was but one of many elements to this twisted tale of government subversion.

Ray, who made his return last night, received a text message that Kort was in Tel Aviv, and to "handle it." Perhaps the one-eyed slime, who co-opted Frankenstein for personal gain, has finally crossed the wrong people at The Company.

Suffice it to say, the box he gave Ziva felt like an empty gesture in more ways than one. CI-Ray may be one of the "good" guys, but he has work to do to win our trust.

The fact that CI-Ray is off to Tel Aviv of all places makes you think, too. As world cities go, that's a random one ... unless his business there somehow involves the Davids.

Mike's funeral, meanwhile, was one of the most moving scenes in recent memory. As many of us posited last week, if Cobb didn't kill Gibbs' mentor, Franks' own lungs were about to. Gibbs knew it, as evidenced by my favorite reveal of the night.

After watching Gibbs in the basement all season, finally seeing his woodwork on display during Mike's burial - with the Marines' gun salute and "Caught By the Light" by The Boxer Rebellion providing the soundtrack - probably left a lot of viewers choked up.

Then came the cliffhanger(s).

Barrett is moving on, or so she says. Gibbs told her she's welcome back anytime, or so he says. From the theft of that chip to Cobb sparing her twice, there's something very much amiss about E.J. Which brings us to Tony and the new SecNav.

Vance and his new boss called Tony in to track down someone within the organization selling U.S. intelligence. Clearly Tony was chosen for a reason, and from the look on his face, clearly he's familiar with whom he's been assigned to keep tabs on.

Kort, Ray, Cade ... there are plenty of possible suspects. But the one I keep coming back to, given the scene in the morgue and Tony's relationship with her, is E.J.

What does Tony know? What will he do? This was a fantastic way to end a season finale that, rather than splitting Gibbs' team apart, brought them closer than ever.

While "Pyramid" was unconventional in some ways, it left me appreciative of the show's underrated writing and acting, and already anxious for Season Nine of NCIS.

Do you agree? What was your favorite part of the NCIS season finale? What do you make of Tony's assignment? Sound off with your comments below.

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