Way, way back in July, we asked Joss Whedon if Dollhouse was saying that nurture trumps nature, and we're all just what we're programmed to be. And now we know. Spoilers ahead.

I'm going to be puzzling over last night's Dollhouse season finale for a long time to come, especially if it's the last televised Dollhouse we ever get. (It's not looking good — possibly thanks to Kirk and Spock, last night's episode hit a series ratings low.) The finale packed in a ton of backstory and weird ideas and freaky scenes, to the point where smoke was coming out of my ears.

But in the end, it all came down to one question: What made Alpha Alpha? And can he repeat the process for Echo, turning her into Omega?

We learned that Alpha was always a troubled Doll, even from his earliest brain-mulching. He always had the crazy eye, and his childlike "Doll" state was more like a demented toy than a friendly lobotomized person. And then the Dollhouse, in its infinite wisdom, decided to program Alpha and Whiskey with Natural Born Killers-inspired serial killer personas, to fulfill a client's particularly self-destructive fantasy. (We only see how the fantasy goes wrong, so we don't know what it would have looked like if it had gone right — but I'm just guessing it's nothing good.) And that helps push Alpha over the edge, causing him to slash Whiskey's face. Then, while Topher is scanning every single one of Alpha's past imprints, he breaks out, causing all of those imprints to be zapped into his brain simultaneously. And he goes on a killing spree, leaving only his beloved Echo untouched.

But of course, that's not the real reason why Alpha was such a broken Doll... even before he was a Doll, he was a convicted felon, Karl William Kraft, who had already been working his way up to being a serial killer. The Dollhouse (again, in its infinite wisdom) decided to test out its mind-blasting tech on hardcore criminals at first, and Kraft was one of those early recruits.

So in the end, it's not the mind-wiping or the having too many brains jammed into his head at once that turned Alpha into a monster. He was always a monster, from the beginning.

Echo, meanwhile, is a good person, who has only been developing her good person-hood during her time as a Doll. Every time she's gone "off mission," she's been getting smarter, better and more compassionate. (And for those of you who think Eliza Dushku's acting is a bit one-note, there's your explanation — it's all been deliberate, to show how Echo is developing a sense of personhood.) Caroline was a good person before she became a Doll, and Echo has been becoming an even better person.

So when Alpha tries to turn Echo into another crazy-face too-many-minds monster like himself, he fails. Instead, he only completes the process of her becoming self-aware. Thus proving, as Paul Ballard puts it, that there is such a thing as a "soul," and you can never entirely erase who someone is at their core. You couldn't put Gandhi into Topher's chair and turn him into Stalin, at least not entirely. Does this mean Dollhouse just completely invalidated its own premise? Or did the premise just get a bit more complicated? (Actually, I think this idea was baked into the cake from the begining, but this is just the first time we're seeing it expressed properly.)

In any case, it's an interesting idea: that we're more than just the sum of our experiences and beliefs and programmed behavior patterns. One of the reasons I've always hated the idea of reincarnation is because I've always felt like if I was reborn with none of my memories, that wouldn't really be "me" any more. Without my memories and all the ideas I've thought of and people I've loved, there'd just be some kind of undifferentiated spark of humanity, which could be anybody. But Dollhouse is trying to make the case there's something else, which is a surprisingly spiritual turn from a show that's been so determinedly secular so far. (Interesting that writer/director Tim Minear wrote the only other Dollhouse episode to deal with religion, "True Believer.")

So Echo finally got to speak for herself and have some perspective on what's been happening to her, and what a relief that was. I think part of me has been waiting the past few months for this moment: for Echo to stand up and show real awareness, and actually take control over all of the fantastic abilities and smarts the Dollhouse has given her. (Am I the only one who was slightly disappointed that Echo and Alpha didn't have a super wire-work-y kung-fu battle, with all their pre-programmed wushu skills? No-shadow kick!) And it was a relief to hear Echo, of all people, point out that you can't sign a contract to be a slave.

Echo's "original self," Caroline, came out a bit better this time around as well. The first time we really got to know Caroline, in the college-campus "Naked Time" episode, she was a major disappointment. So it was a relief that when Caroline's "imprint" got programmed into a poor random sales clerk, we got to see her being a bit smarter and feistier. You can especially see it in the clip above, when she gets some classic Whedonesque lines about being in an evil lair, with a guy who talks to himself attaching electrodes to people's heads.

Alan Tudyk, by the way, was pretty great as Alpha. It can't have been that easy a role to play, especially trying to convey that Alpha isn't a "multiple personality" in the classic sense — he's 48 completely formed, always present personalities. (One of which is a multiple personality.) Tudyk gave one of his all-time classic demented performances, except this time he was actually dementedly scary and intense.

I'm not entirely sure I buy Paul Ballard's change of heart, meanwhile. It just needed a bit more groundwork or something. Ballard suddenly goes from wanting to destroy the Dollhouse to wanting to work for it — I get it, he feels responsible for bringing Alpha there, and he has some kind of Prince Charming thing around wanting to save Echo/Caroline. But I wasn't sure why Ballard wouldn't just save Echo and then destroy the Dollhouse. It's a bit random, really. (Of course, I had similar issues with Angel suddenly deciding to go work for Wolfram & Hart — in another Tim Minear-written episode, and that turned into a season of fascinating stories.)

I did love the way Ballard got rid of the FBI people — he told Romo Lampkin the truth, knowing that Romo would never believe him. Funniest scene ever.

At least Ballard did the classy thing — instead of bartering his Dollhouse service for Caroline's freedom, he chose to set free the Doll he'd actually had a relationship with already, November/Mellie. I wonder if their fictitious relationship would be touched on at all in a second season, if one happened. I'd actually love to see some stories about November going back to civilian life, and discovering that people remember her from all her engagements, including people who saw her as Ballard's girlfriend. And meanwhile, Ballard might not be able to avoid running into her occasionally. (Of course, if I was a former Doll in L.A., I'd move to Portland or Providence ASAP.)

But even if Ballard's change of heart felt a bit too convenient, it did give us the awesome buddy-cop bromance with Boyd I've been longing for all season. Just the moment where Ballard asks Boyd if he can drive and Boyd says, "I can do that," gave me little flutters of excitement. Those two had pretty much instant chemistry together, and it would be fantastic to watch their adventures (fighting crime, perpetuating human trafficking. Good times) every week.

And yes, everybody who said that Claire was actually a Doll named Whiskey totally called it. There was a Dr. Saunders before her, who was a nice, lollipop-dispensing guy. And then Topher slashed her face, and the Dollhouse decided to salvage her and turn her into the new Dr. Saunders. It was awesome to get to see Amy Acker being glamorous and dangerous again, as the other half of the Natural Born Killers duo. So what does Dr. Saunders do now with the knowledge that she's actually a Doll, and this isn't her "real" personality? Apparently, judging from the little snippet at the end, start handing out lolllipops and being nicer to the other Dolls. (And her question to Topher was one of the most intriguging things in the episode: why did he program her to hate him? Also, Topher looked like his mom had died at the end of the episode. Which of this episode's huge revelations freaked him out so much?)

Speaking of which, poor Victor. What are they going to do with him now? Is he going to turn up programmed to be a backup Topher, or a new, non-evil Mr. Dominic? The bit where Claire told Topher he can't be his best any more, because he's ugly, was pretty heartbreaking. Maybe he can become Roger the suave English dude permanently, and Adelle can keep him squirreled away at her beachside house for when she needs to escape for a little while.

So all in all, I thought this was a pretty good episode. Not the best of the season, by any means, but pretty thought-provoking. After I wrote that thing yesterday about Dollhouse being Joss' greatest work ever, I was crossing my fingers for this episode to be awesome, so I wouldn't have to eat crow. Luckily, it was mostly pretty great.

I say "mostly," because of the Ballard change-of-heart, and because of some pacing issues. As with a lot of episodes of Dollhouse, this felt slightly stretched out to fill the "remote-free viewing" schedule. (Dollhouse and, I guess, Fringe have been running with fewer commercials, meaning episodes are quite a bit longer than usual TV shows.) I could have used slightly less Alpha speechifying, and slightly more explanation of why Ballard chose to do an about-face. Also, what on Earth happened with Sierra and November being programmed to be "bounty hunters"? We know they filmed some more scenes of those two doing the bounty-hunting thing, because the studio released some promo pics of the duo being all Boba. So what happened?

All in all, though, it was a terrific season finale, which I'll probably be rewatching and rethinking for years to come. It sets up a status quo that would be tremendously fun to watch if a second season actually materializes — Echo retaining a ton of awareness and being newly empowered, Ballard being a sell-out and getting to bromance Boyd, Claire Saunders knowing she's a Doll, Victor being all scarfaced, and Topher maybe finally growing a conscience, or something.) As the Fox execs have been claiming all along, this episode serves perfectly well as a season ender, and the unaired post-apocalyptic episode "Epitaph One" is sort of an unrelated add-on. And yet, I have a strange feeling that "Epitaph One" will provide a lot more thematic closure to Dollhouse than this episode did, perhaps showing us exactly how that future apocalypse happens, and how Echo and her friends play into it. I am now officially on tenterhooks, waiting for the DVD.

What did you guys think?