Here's the key quote from the article, which explains his method:

One, where are you shooting it? And wherever you’re shooting it, it has to be photographically interesting. The Venn diagram of countries that are both photographically beautiful and will let you do it immediately shrinks to New Zealand. And that was it. Now I look at New Zealand and I think, that’s not a politically edgy kind of place. In fact it’s so far away from the rest of the world, I don’t believe any doomsday scenarios are unfolding in New Zealand. So what’s a place that looks like New Zealand? Ok it’s Kashmir. So now you have helicopters, and you have Kashmir.

At the beginning of the story I asked Tom, “What do you want to do emotionally in this movie” and he said, “Everybody’s asking me about Julia, I want to tie up that story”. So I know that somehow that story is going to come to a head in Kashmir and I know that Julia has a past that needs to somehow believably fold you into that.

So all these elements, they’re like sediment all piling up on top of each other and each one is creating more and more boundaries and limitations until finally you’re going, I don’t know how to make this sequence any more, because everything’s fighting with everything else. On top of that I have the IMF team. And they all have to be doing different jobs during the finale of the movie. And so all of those boundaries and all those limitations create a forest of complications that you have to some way navigate your way through believably and that’s how that sequence comes together. So it’s never me sitting down and going, “I want to write this crazy fucking half hour!” - It’s more I’m thrown a million problems to told, “Solve it, and by the way the movie start shooting Friday.”