Now we learn that his cooperation was squirrelly and incomplete, a series of prevarications that obviously infuriated the prosecutors, who gave him one final 10-day chance to play it straight. But he did not heed the warning and now is unlikely to ever leave prison absent a pardon from President Trump. Which leads us to:

Hypothesis No. 1: The Pardon Promise

Did the president secretly promise to rescue Mr. Manafort, so long as he resisted Mr. Mueller? That would make sense of his otherwise confounding conduct. But the chain of implausibilities is long.

The prospect of a pardon was always in the mix, including when Mr. Manafort made his initial decision to cooperate. For it to suffice to change his mind now, it would have to have become all the more certain. But that would entail some communication, from the president, through two intermediaries (one in the Trump camp and one in the Manafort camp) and on to Mr. Manafort in prison, where all his conversations are monitored.

The perils for all those participants in such a crass scheme would be enormous. If discovered, it would mean assured conviction for witness tampering and, if any of the intermediaries was a lawyer, disbarment. For the president, it most likely would trigger impeachment, and even conviction in the Senate could not be counted out. Finally, for Mr. Manafort, it would require a measure of Mr. Trump’s good faith that nobody acquainted with the president’s track record could comfortably have. And it would still not shield him from near-certain prosecution for related state crimes.

Hypothesis No. 2: The Assassination Fixation

Some commentators have suggested that Mr. Manafort’s lifetime of shady dealings with the Russian government have left him more afraid of life on the outside, where he could be vulnerable to a poison needle anytime, than of the safe confines of a federal prison.

This scenario was always out of the most imaginative Le Carré novel, and it is the sheer unlikelihood of the other alternatives, combined with Mr. Manafort’s intransigence, that makes it a contender at all. The problem with it at this point is that there’s no reason to think that any of the cloak-and-dagger circumstances would have changed. If Mr. Manafort most feared the spy’s comeuppance, he wouldn’t have agreed to cooperate, and earn a much reduced sentence, in the first place. So that hypothesis doesn’t help explain Mr. Manafort’s decision to double-cross Mr. Mueller.