Forget all the stories explaining how the election imperils the New START treaty.  The elections matter, but not quite in the way you think.

The real threat to the New START treaty is now from the nuclear-weapons complex — comprising  NNSA, the labs, and the production facilities — which is poised to blow up the bipartisan consensus in favor of both the New START Treaty and modernizing the nuclear-weapons complex, over a wafer-thin mint.

The issue is whether to insist on a multi-year appropriation for the nuclear-weapons complex.

Whatever you think of the President, the Prague Agenda or New START,  the Administration has succeeded in establishing a bipartisan consensus on nuclear-weapons policy featuring reductions to New START levels, with substantial investments in the modernization of the US nuclear-weapons complex.

This is a pretty good deal for NNSA, the national laboratories and the rest of the nuclear-weapons complex.  They have gone from open warfare with their appropriators in Congress during the Bush Administration to a Presidential commitment to spend unprecedented sums on modernizing the nuclear-weapons complex. The Administration pushed Congress to pass a Continuing Resolution for the budget — which typically funds government entities at the previous year’s level — containing increases in NNSA’s budget. There is a reason that Linton Brooks told the Exchange Monitor that “I would’ve killed for this kind of budget.”

But that wasn’t the entirety of Linton’s quote, which is actually very revealing about the current impasse over New START:

No organization in the history of government has said, ‘Oh gee, I got too much money.’ I’m sure somebody can find something they wish was in there but I would’ve killed for this kind of budget.

That is, apparently, exactly what is happening: some little birds in NNSA are finding new wishes, one after another.  Now, there is always some WeeBee who will don the mantle of “responsiveness” to Congressional interest and cook up some scheme to get a little more dough.  It now appears NNSA is arguing that recent flooding at PANTEX, among other unexpected requirements, will eat into this year’s budget.  Are asking yourself: Is NNSA really about to kill the goose that laid an $8 billion egg over $60 million in flood damage?

Yes, apparently some of them are!  The little birds at NNSA appear to be speeding toward this precise cliff. Senator Kyl, prompted by sources inside NNSA, is now mulling over whether to demand another delay in ratification, followed by a multiyear design/construction appropriation next year to guarantee that the money will be available in future years. Did you know Congress could do that?  Yes, they can! (Here is a nice primer on the topic.) But Congressional appropriators almost never do, since the annual appropriations process is an essential element of  Congressional oversight.

The House and Senate Appropriators are going to refuse such an obvious usurpation of their prerogatives. That means that the little birds at NNSA probably can’t win the battle over multiyear appropriations, but it can blow up the entire deal.

And, in doing so, the little birds at NNSA will destroy the bipartisan consensus tentatively established by the Obama Administration. The lack of a bipartisan consensus on US nuclear weapons policy during the Bush Administration was a catastrophe, first and foremost for the national laboratories.  There wasn’t much good news for arms control in this period, but the open warfare between the labs and their congressional appropriators was terribly damaging.  A Republican Congress refused to fund the Robust Nuclear Earth Penetrator and Reliable Replacement Warhead, and recompeted the contract for Los Alamos National Laboratory, which the University of California had held since the inception of the Manhattan Project.  This was the era of layoffs, LANL: The Real Story, and Tommy Hook getting beaten up at Cheeks, to say nothing of documents turning up in meth labs and diffusion barriers in the trash.

Yet, that is where we are headed.  Of all of the stupid, self-destructive things the nuclear-weapons complex has done over the years, this would take the cake.

There are two key figures in whether the deal sticks, or not.

The first is Senator Kyl.  The Administration is making it clear that their strategy goes through Senator Kyl.  But Kyl is enigmatic:  Is he really looking for a deal on modernization, or is he just looking for a reasonable sounding excuse to torpedo the treaty?  The elections matter because Kyl is not just some Senator, but serves as Senate Minority Whip and, presumably, has higher ambitions.  His calculation is partly about New START, but also about his future role in the GOP.  He has to worry about covering his right flank from the likes of Jim DeMint, who is committed to dancing with Tea Party.

I continue to think that, given a stark choice between a well-funded nuclear-weapons complex or a talking point about how the Obama Administration is unilaterally disarming the United States, Kyl is ambivalent — particularly if DeMint is chirping at him from the right.  That’s why the little birds at NNSA are playing such a dangerous game in spinning up Kyl.  At the end of the day, Kyl wins either way.  The nuclear-weapons complex will be holding the bag.

What Kyl does not want is a deal without him.  That makes him irrelevant, instead of indispensible.

Which brings us to the second figure — the President himself.  He needs to start by learning to ride herd on his own damned bureaucracy — the number of openly disloyal political appointees is stunning. (Apparently, many fear the wrath of Republican Senators in a future confirmation more than the President himself, which is a bad sign.) From his initial decision to hire General Jones as National Security Advisor, he has shown an amazing lack of appreciation for how bureaucracy can stymie Presidential ambitions.  (Can it be that Barack Obama has never seen an episode of Yes, Minister?)

But after getting tough with his own team, Obama has to begin aggressively reaching out to Republican Senators directly, not merely relying on finding a magic formula for Kyl (which might not exist), or hoping that others, like Senators Corker or Lugar, will do his dirty work for him.

I continue to think that the Administration was clever to front-load most of the benefits in the budget as a way of reducing the partisan temperature over New START.  And, clever or not, it is hard to imagine someone of Barack Obama’s temperament handling it any other way. But this is the end-game, where you count votes and grab lapels, threaten and cajole.  An air of inevitability is crucial.

If there was ever a time for Obama to find a little Lyndon Johnson in him, this is it.

Update | 1:27 pm Stephen Young at All Thing Nuclear notes that the Secretary of Energy’s independent review of the Chemistry and Metallurgy Research Replacement Nuclear Facility (CMRR-NF) and the Uranium Production Facility (UPF) might be the stick to all the carrots.