The ninth season premiere of NCIS was slower-paced and more complicated than expected, but provided a compelling conclusion to Tony's mole hunt while setting up a new foil, and a new enemy, for Gibbs.

It takes consistently strong writing and characters to pull off an episode like "Nature of the Beast" without making certain plot elements - interdepartmental politics, temporary amnesia, Scott Wolf - feel hokey.

That's NCIS for you, though. Just when you think you have it figured out, you don't. Not by a mile. Time and again, we're thrown curveballs that not only change the game, but the rules it's played by, and the players who call the shots.

Tuesday was no exception, and it was superb.

The episode struck a serious tone from the onset, and was devoted entirely to tying up the mission Tony was assigned in May, which itself was an offshoot of the P2P Killer storyline they just resolved.

What resulted was a very strong episode and plenty of questions answered, but also more loose ends to say the least. The mystery of the Phantom Eight goes deeper than anyone (but Gibbs) realizes.

So what did Tony spend his summer doing? We certainly didn't find out in haste, given that he woke up in the hospital, literally, with blood on his hands, not to mention a bout of short-term memory loss.

Michael Weatherly, of course, sold this well enough to make it work, alternating between goofy DiNozzo, cracking jokes while barely conscious, and starkly recalling the chilling memories of where he'd been.

With the help of Wendy McKenna's Dr. Rachel Cranston, he put the pieces together. The flashbacks were all effective, even if it made for drawn-out storytelling and much less action than I anticipated.

Cranston felt a bit out of place to me, even though I like the character. Yes, Tony and Gibbs have a relationship with her, but given her connection to Kate, it almost felt like she was a distraction last night.

What also felt strange to me was the team's disbelief that Tony was assigned a secret mission. Isn't that what they do? It would be a little unusual, certainly, but not out of the realm of possibility.

Gibbs being peeved that Tony was being used without his knowledge - let alone manipulated as a pawn in a high-stakes chess game and put in grave danger - I can see. But the rest of the team?

For half the episode, we were led to believe Tony was targeting E.J. and may have even killed her, especially due to the trauma he suffered. He was indeed after her, but there was obviously more to it.

The nuances of who knew what and when were very hard to follow, but entirely realistic. This felt more like a murder mystery novel than a TV show at times, but the action eventually picked up.

E.J.'s shadiness in stealing the microchip wasn't as sinister as we were led to believe. She was fulfilling a request given to by her fallen agent, Levin, while people far above her pay grade had other ideas.

Tony eventually realized, quoting Rule #36, that he was being played. So were E.J. and Cade - later revealed as the agent in the photo. SecNav Jarvis basically confirmed as much. But by whom? And for what purpose?

Scott Wolf's faux FBI agent felt dirty from the start, and even dirtier the second time he showed up to finish the job. Gibbs smelled it a mile away and Fornell (fun that he got a mention) confirmed it.

Agent Stratton was working with Latham, head of the ONI's Watcher Fleet. The extent of their machinations wasn't overtly explained, but they're selling classified information, and thanks to Mike, Gibbs is on it.

When he basically told DiNozzo, by evoking the episode title, that he could be collateral damage, SecNav Jarvis showed his true colors. It'll be interesting to see Gibbs clash with him again, which I'll bet happens before long.

Vance may be a company man, but I never took him for a true backstabber who's out to get Gibbs, despite their differences. Jarvis may be a different story. And then there's Stratton, or whatever his real name is.

How do you think he'll be brought back into the fold, which the chilling, episode-ending montage teased so eerily? He seemingly got away without a trace, and would want nothing more to do with NCIS.

Of course, we know it's never that simple, especially with Leroy Jethro Gibbs onto you. Seeing him in the photo was a terrific conclusion to a season premiere that, despite a few flaws, was still rock solid.

A few random thoughts on last night's episode before I turn it over to your feedback:

• Wendy McKenna looks like she could be related to Sasha Alexander.
• The discussion of Tony's "complicated relationships" was priceless.
• "You two are cut from the same quilt." - Amazing.
• Rules cited last night: #3, #5, #36.

What did you think of the NCIS season premiere? Leave a comment below!

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