If the reports I've read about the closing arguments are any indication, there would seem to be a fair chance that Padilla will be acquited. As Lithwick says, the evidence seems to consist largely of indications that he wanted to be a terrorist plus wiretaps that the government insist are referring to him even though his name isn't mentioned. That seems like a tough sell.

That makes me wonder what the Administration's backup plan might be. Padilla clearly is someone they don't want released - his story is both frightening and compelling, and if he's given the opportunity to tell it, many people will be appalled.

Given these constraints, you have to think the Administration will do whatever it can to keep him under wraps. My bet is that the dirty bomb story would come back, and they'd try to charge him for that, hoping that the trial could be put off for another year or so. They might also tack back into enemy combatant territory, perhaps moving him to somewhere outside the suddenly-not-so-compliant 4th Circuit so that they can get a new chance to make their enemy combatant arguments. (I'd vote for the 8th Circuit, actually.) Whatever they do, they certainly won't let him go.

If he is Acquited, double jeopardy comes into play unless there is another charge for another crime that can be brought in. Unless he could be detained elsewhere, and there would be huge uproar over that. If he is acquited, he most likely walks. What effects would that have on people who mihgt have similar plans? Who knows. Maybe terrorists would try to recruit more US Citizens because of the legal system being preferable to Gitmo if they are caught. With luck he will be convicted if guilty (He probably is, but as you said proving it in court is another thing entirely - Look at OJ Simpson amd the current Spektor case in LA) the alternative might be a Padilla who is free to go, and spends the next how many years openly crowing about his plans and what he did, and how he got away with it - and telling others to join him.

My thinking was that the government would avoid double jeopardy by going back to the dirty bomb claim, which the prosecution carefully avoided mentioning even once in this case.

Based on other articles I've read, it sounds like Padilla barely functions at all right now, and that he's in no state to crow about anything. Of course, that could be a subterfuge, but it seems unlikely on the information that's been made available so far.