What caused "The Operative" to support Mal's team at the end of the movie?

Question

Until at the end of the Serenity (2005) movie, "The Operative" caused obstacles to Mal's team.

What caused "The Operative" to support Mal's team at the end of the movie?

Answer 1

There are two significant reasons why the Operative chooses to spare the crew in the end. Both are tied up in his self-image as someone who knowingly, reluctantly, does terrible things in search of a better future.

The Operative: I believe in something greater than myself. A better world. A world without sin.

Mal: So me and mine gotta lay down and die so you can live in your better world?

The Operative: I'm not going to live there. There's no place for me there, any more than there is for you. Malcolm... I'm a monster. What I do is evil. I have no illusions about it, but it must be done.

Throughout the movie, the Operative is guided by his belief that this "better world" requires that River Tam be silenced before she can spread the word about what she knows to the rest of the 'verse.

So, the first reason he spares the crew is that he has already failed and they have won. Their message, with the evidence they took from Miranda, has already been sent. The Operative can no longer stop the threat it represents to his better world - all he can do is get revenge. That isn't the kind of person he is.

The second reason is that ironically, the broadcast has shaken his faith in the Alliance regime. He has seen a glimpse of what the Alliance's "better world" would look like, and what it might cost, and has started to wonder whether the one is worth the other. This is what Mal alludes to when he says he will give the Operative his greatest wish: to show him "a world without sin".

Answer 2

The operative states that he's willing to commit atrocities for the greater good, to help form perfect worlds free from 'sin', a concept he brings up multiple times.

Finding out that River Tam knows a secret due to someone's mistake:

THE OPERATIVE

It's come to our attention that River became much more unstable, more... disturbed, after you showed her off to Parliament. Did she see something very terrible in those cards?

DOCTOR MATHIAS

Whatever... secrets she might have accidentally gleaned... it's probable she doesn't even know she knows them. That they're buried beneath --

THE OPERATIVE

But they are in her. Her mind is unquiet. It's the will of the Parliament that I kill her. And the brother. Because of your sin.

And later when talking to Mal:

THE OPERATIVE

You know what your sin is, Malcolm?

MAL

Aw hell, I'm a fan of all seven.

The biblical imagery continues explaining how he sees himself:

MAL

Don't talk at me like a righteous man. You are a killer of children

THE OPERATIVE

When God wanted Pharaoh to release His people from bondage -- you know the story? He didn't ask. He sent his plagues down upon Egypt. That's me, Captain. The path to peace is paved with corpses. It's always been so.

Next The Operative clearly shows that even he doesn't see himself as free from sin, far from it:

THE OPERATIVE

I'm not going to live there. How could you think -- there's no place for me there, any more than there is for you. Malcolm, I'm a monster. What I do is evil, I've no illusions about it. But it must be done.

But in his work he doesn't question his orders, believing his orders are unquestionable:

MAL

Why? Do you know why?

THE OPERATIVE

It's not my place to ask.

But later on, when he's forced to watch the outcome of an actual literal plague. Not of frogs, or locusts but G-32 Paxilon Hydroclorate.

And Mal shows him this plague from the recording they recovered:

MAL

I ain't gonna kill you.
Hell, I'm gonna grant your greatest wish.
I'm gonna show you a world without sin.

As the recording he watches shows:

well it works... it was supposed to calm the population, weed out aggression. Make a peaceful... it worked. The people here stopped fighting. And then they stopped everything else. They stopped going to work, stopped breeding... talking... eating... There's thirty million people here and they all just let themselves die. They didn't even kill.

By The Operative's logic, had some of these been sinful people it could have been justified, even with huge collateral death. Had it worked to create a perfect world, even if he wasn't part of it, his twisted morals would have allowed him to be part of it. But not only did that not happen, but also it was instrumental in creating:

The Reavers

As the next part of the recording shows:

There are people... they're not people... about a tenth of a percent of the population had the opposite reaction to the Pax. Their aggressor response increased... beyond madness. They've become...

When the operative learns this shattering truth something in him breaks. He knows he's no longer working for unquestionable masters, who's only goal is a peaceful world. He knows that this 'world without sin' isn't possible, and that it was never the Alliance's goal (instead that wanted a passive population to control.) And that the collateral was too great.

All of his monstrous actions, for nothing.

He lets Mal go, knowing that at least there is no longer a secret in River Tam's head and at most that he no longer has the moral high ground to use any means necessary in following his previous order.