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The Special Counsel's office, nearly leak-proof since its inception more than a year ago, can appear to be operating in some parallel universe unmoved by the every-day political turmoil. But in the course of conversations I've had researching a new book on President Trump and the forces arrayed against him, it has become clear that Robert Mueller and his office are already preparing for a life or death confrontation with the President and the mother of all constitutional crises.
Over the last several months the Mueller office has prepared a possible indictment of the president on charges related to obstruction of justice and devised a legal strategy to navigate the inevitable fallout from such an indictment.
My discussions have been with both White House advisors and people close to the investigation—that is, sources on both sides of the possible conflict. No source involved in this story would speak on the record. But in broad-strokes each side's understanding matches the account provided to me by the other side.
Since at least April the Special Counsel has had in place a set of allegations, proposed charges, and an aggressive legal theory to support the indictment of the president on obstruction charges. In the last few weeks, as the President has indulged his pardon authority, the Mueller team has also developed a legal basis to oppose what the Special Counsel believes will be a likely pardon of former National Security Advisor, Michael Flynn—who had previously struck a plea bargain which could include his testimony against the President—and what it believes to be another step in the President's obstruction efforts.
At this point, the case for indictment has, in effect, a judge of one, since the Mueller team must get the approval of Deputy Attorney General Rod Rosenstein to proceed. As recently as April, Rosenstein publicly declared that the President was not a target, but this may have been a kind of fig leaf: technically the President does not become a formal target until Rosenstein agrees to designate him as one. It may also illustrate a conflict between the Deputy Attorney General and the investigators he has overseen since the recusal of Attorney General Jeff Sessions from the Russia-related investigation—though, according to one source, Mueller believes he does have the support of his boss.
The proposed indictment would be all the more controversial because it finds the entire narrative of the case for obstruction in plain sight. Almost nothing in it-involves new information; rather, it takes well-covered public events and moves them to a set of circumstantial

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