In the Flynn case, the prosecution and defense both agree that the case should be dropped. Because there is no longer any controversy between the parties to be resolved, there is no longer any case properly before the judge. His only job is to enter an order vacating the guilty plea and dismissing the case with prejudice.
[Sullivan] is endangering our system of separation of powers and he should be stopped by a writ of mandamus or a motion to recuse. Judges, too, are not above the law or the Constitution.