Impossible as it sounds, Judge Denise Cote has found a way to make the Justice Department's antitrust assault on Apple even more abusive. Because it presumed to enter the e-books market, the court is forcing the company to pay for a special prosecutor to investigate itself—and shredding the separation of constitutional powers too.

In July, Judge Cote of the New York federal district court convicted the iPad of being a conspiracy to increase digital book prices, though the tablet's 2010 introduction increased competition and...