While on tour in 1998, Thom programmed the first musical idea for this song on his QY70 sequencer. An excerpt of this version can be heard in Meeting People Is Easy during the Australia segment. During the same section Thom can also be seen working with the QY70 in Australia:

According to Thom, the lyrics were inspired by "watching the delights of Rwanda on TV". The war in Zaire, that involved Rwanda, began on august 2nd 1998. This would fit with Thom saying in 2003 that it was written "5 years ago". But his Rwanda comment could also very well refer to the genocide in 1994, which would perfectly fit the "wipe you out" references. In that case the lyrics would be much older, and he perhaps only refered to when the music was created in that 2003 interview.

The song was probably attempted in the Kid A sessions, but it's highly doubtful that the working title was 'Innocent Civilians', which appears to be a different song, which is perhaps similar in terms of lyrics and music.
At any rate, lyrics that put the phrase "innocent civilians" next to lyrics that would end up in 'Sit Down. Stand Up.' could be found in the late 1999/early 2000 version of radiohead.com in a page titled 'collaterally damaged', that appeared in two designs:

Thom recorded a very slow demo of the song in late 2001 or early 2002, but the song changed drastically in the following rehearsals in spring, with the pace increasing vastly and the focus being put on rhythm.

When played during the Iberian Tour in 2002, the song got wild response from the audience each time. This performance is from July 30th 2002 in San Sebastián, Spain:

2002 Iberian tour

july 2002

august 2002

	Sit down Stand up [10]		23	24	26	27	30	31	01		05	06	07
	We suck Young Blood [9]	22	23	24		27	30	31	01		05		07
	I will [3]	22		24		27
	A Punchup at a Wedding [10]	22	23	24		27	30	31	01	03		06	07
	Scatterbrain [9]	22	23		26	27	30	31	01		05		07

In September 2002, when the band attempted to capture the energy of this arrangement on tape, it somehow didn't work anymore. So the song was rearranged, especially from the explosion in the middle onwards.

On March 30th 2003, the rough mix of the song leaked and it represents the state of work from February. In this version, the drum beats enter much later than in the released version:

In 2003, a heavily processed sample of the words "the rain drops", that probably isn't related to the Hail To The Thief version of the song, but perhaps an earlier incarnation, was made available in the Loophole section of radiohead.com (the loop was called 'R145'):

If the above sample comes from an early, slower version of the song, then another sample preceeding it in number, 'R143', might be taken from the rhythm track of the same version, but this is speculation:

This association of both samples is supported by the fact that, if dubbed on top of one another, both samples align perfectly. It is possible that this yields a glimpse of Thom's demo of the song:

Thom: "It was sort of written initially... the demo I did of it for the others was very, very, very slow, indeed. And I kind of wanted it to keep that in, keep this sort of like chanting about it, really. And the words weren't really relevant, it was just these melodies going 'round and 'round against each other, you know. I'm not quite sure where that came from, but it's probably kind of a Mingus thing, one of my many Mingus hang-ups from another Mingus track. But then it just turned into this blimming, I don't know, rhythm fest thing. because it was obviously not gonna stay like that, I don't know... It's very, very old as well. I mean, it's pre-Kid A, the initial idea for the song. And the 'rain drops' section just came out of thin air, I don't know where the hell that came from, to be honest. Got no idea.
It was a series of... I mean, virtually everything on that track scarily is from one take. Except obviously the other vocals. I mean, all the instrumentation and everything. And when we were playing that live we were getting this insane response, and we didn't know... 'cause we went out and we tried out all the songs before we recorded them, you know. We went to Spain and Portugal and played all these things. And 'Sit Down. Stand Up.' always used to... I mean, it was such a joke, because, you know, the last 2 minutes of the song we just didn't know what we were doing. We didn't have a clue, you know. Jonny was like sitting there on his big AS machine, and all the lights flashing, Phil was trying to work out where he'd left the beat, and me and Ed are just like 'well, let's just keep singing 'raindrops', and hopefully people will think that it's coherent, even when it's not. And that's basically what we ended up with, really. But then we went into this sort of thing where we had this... there was one section where we basically cut it all into shreds and put it through the laptop and spat it back out, and kind of thought it was really too silly. But Nigel was like 'no, no, that's gonna go in'. And he was right, he was really good. It just switches into this other mode completely, like someone switched on the calculator and made everything quite rational, and then it's kind of not. I don't know. It's something I'm very proud of, but I just can't remember how the hell we got there, to be honest, like with most things on this record."

Phil: "That song was recorded in the first week of recording. That was actually... probably went through more processes than any other of the tracks on the album. We got the main performance down on the day it was recorded, and then we had this... it was brilliant, it builds and builds and builds. And you get to that section in the middle, which just explodes into this kind of electronica thing. And it was just fizzled out at that point. And fortunately it was just coming down to me doing this very, you know, beautifully played, of course, but it was a very lacklustre pattern. And so that section there... it was just trying to find something there, that maintained and built on that intensity, as we're going through."

Colin: "I think you're being a bit harsh on yourself about that, though, so... it's just one of those things where... we played it live before we recorded it and it was like, we got really big PA and it's like, we had a plot worked out. But then we took that plot into the studio, and we didn't record it how we'd been playing live in that section properly, whatever, with all these voices and stuff. Just didn't work out, so we changed it.
I like that song because of the James Bond beginning as well, with this electric piano sound, that Jonny plays, doing this Glockenspiel thing or whatever it is. And it sounds like the beginning of 'Diamonds Are Forever' or something."

Thom: "That was written five years ago, in fact. Post Ok Computer, around the delights of Rwanda, watching that on TV."

Jonny: "A lot of the lines and lyrics are a lot older than people are assuming, I think. Like 'I Will' is from five years ago. In the lyrics I hear confusion and escape, like 'I'm going to stay at home and look after the people I care about/Buy a month's supply of food.'."

Thom (laughs): "Spot the new father!"

Jonny: "So I think it's wrong to think there's a coherent thing running through the album. The whole thing ends, for me, with a bit of a shrug."

Q: "What can you tell us about 'Snakes & Ladders', as it's otherwise called?"

Thom: "Oh, right. Don't know… That was one of the titles for the record that kept running around, but didn't make it. When I sing it though, I always think of the 'We can wipe you out anytime' line. And they've developed that missile now that they can just launch, and target it on the strength of your mobile signal. Then they wipe someone out on that. They did that before the Iraq war. They did that. It's pretty impressive. And that's what I always think of… be careful what you say. Be careful what you say on your mobile phone. Not that I'm paranoid or anything…"

Thom: "[The lyrics] are very much just absorbing what's going on around. There are two or three old songs in there that never made sense until now, like 'Sit Down. Stand Up.' and 'I Will.' You just absorb. You can't help it, even if you try not to. I tried not to. I desperately tried not to write anything political, anything expressing the deep, profound terror I'm living with day to day. But it's just fucking there, and eventually you have to give it up and let it happen."