As he spoke, Cote—an owlish 67-year-old woman—barely budged, but reddened. And when Snyder attempted to pivot to the substance of Apple's defense, she quickly cut him off. "Excuse me, Mr. Snyder," she began softly, in a voice which, even after four decades in New York, still betrays a hint of Minnesota. "I wouldn't want Apple to begin this three-week trial thinking that it was going to get anything other than a fair hearing." She'd be all ears, she pledged: the deck wasn't stacked against Apple unless the evidence was.

The trial proceeded pretty much as planned, right down to the minute, as things before Cote invariably do. And then, scarcely three weeks after closing arguments, came her opinion, all 160 pages of it. For Cote, such extreme efficiency was standard operating procedure. For Apple, though, it was all a bit too quick, as if parts of it had been preordained. And sure enough, if anything, what she'd heard in court had only hardened her views.

The publishers' conspiracy to wrest e-books out of Amazon's control, she wrote, would not have worked "without Apple's orchestration." It was Apple which, by introducing an electronic bookstore with its new iPad, and meeting with the various publishers, had provided "the vision, the format, the timetable, and the coordination" the publishers needed to raise e-book prices. Cote dismissed the claims of various Apple executives and publishing chieftains that they'd not been in cahoots. Several she essentially labeled liars.

For Cote, a figure beloved around her courthouse and in the fraternity of former federal prosecutors in Manhattan, the decision brought rare attention, and censure: both The New York Times and The Wall Street Journal accused her of bollixing up the marketplace and protecting a monopolist. Already Cote had been vilified by the book publishers, a strange twist for one of the most voracious readers in the federal judiciary. Though coming into the case after three of them—HarperCollins, Hachette, and Simon & Schuster—had settled with the Justice Department (Penguin and Macmillan capitulated later), Cote had to approve the deals with all of them, which she did despite the objections of hundreds of booksellers, authors, agents, and small publishers, who argued that Amazon's dominance endangered them. "Amazon sells books the way it sells diapers and garden hoses—as commodities," wrote one novelist, Roxana Robinson. "Turning over the book industry to Amazon would be like turning over the education system to robots."

The sanctions Cote imposed on the publishers—not only $166 million to compensate those who bought books at inflated prices but requirements that executives accustomed to cozy lunches at the Union Square Cafe and similarly swanky spots log and report their chats with one another—chilled the book business. As did her unusually pointed insistence that the testimony of two key executives, Carolyn Reidy of Simon & Schuster and John Sargent of Macmillan, could not be believed.

The industry's supine response to Cote's ruling—Reidy and her lawyers have said nothing, while the normally outspoken Sargent has, with considerable difficulty, managed to muzzle himself—reflects the fear that the judge, who will monitor the publishers' compliance with her order for several years to come, still elicits from the industry. But as three appellate judges weigh Apple's appeal, Cote, too, will be scrutinized. While not appearing explicitly in the appellate briefs, what so many people most admire about Cote—her adamantine sense of right and wrong—will be one of Apple's key complaints.

Since introducing the Kindle in 2007—and setting e-book prices at, or more often substantially below, its own costs—Amazon has wreaked havoc, and panic, among publishers. Beyond devaluing lucrative hardcover books, such rock-bottom prices have helped destroy the "brick-and-mortar" stores where books are showcased. Nothing the publishers did—delaying the release of e-books, complaining to Amazon, upping their wholesale prices to the company, or, in the case of one house, Hachette, actually going to the Justice Department to gripe—seemed to work.

But Apple offered salvation. By opening up an iBookstore in tandem with the new iPad, Apple could "trounce" Amazon, Eddy Cue, the Apple executive who'd pioneered iTunes and other Apple content stores, wrote Jobs in late 2009. Jobs quickly signed on. But Cue had to move fast: the iPad was to make its debut on January 27, 2010, and Jobs wanted to unveil iBooks with it. And Jobs himself was dying.

To each of the Big Six publishing houses, Cue offered the same deal: rather than selling e-books wholesale and letting retailers price them, the publishers themselves would set e-book prices; Apple would only be an agent, collecting 30 percent of sales. By January 26, five of the publishers—only Random House refused—had agreed. Amazon, too, quickly fell in line. E-book prices quickly rose. Soon came the lawsuits—class actions on behalf of consumers; cases filed by various state attorneys general. And then, in April 2012—largely, Apple has charged, at Amazon's instigation—came the Justice Department's case. All said Apple and the publishers had conspired together in violation of federal anti-trust laws.

Cote had had huge, and hugely important, cases come before her before, but they'd rarely escaped the business pages. Reinforcing her obscurity was her reticence (Cote declined to speak to V.F. for this story), which makes her sometimes seem, even to friends, out of another time and place. Her childhood, in St. Cloud, Minnesota, was one of Cherry Cokes and glazed doughnuts after school. But the real world—Freedom Riders, Soviet missiles in Cuba, the New Frontier—seeped in. From the Benedictine nuns she learned that everyone deserved love, respect, and freedom. She remembered, too, the promises, and commands, of John F. Kennedy's inaugural address.

She graduated from St. Mary's College in Notre Dame, Indiana, in 1968, earned a master's in history from Columbia, and, for three years, taught Catholic-high-school students in New York. But convinced that the city, sinking into crime and penury, needed her help, she enrolled at Columbia Law School, where she graduated near the top of her class. After eight years as a federal prosecutor in Manhattan and six years in private practice, she returned to the U.S. Attorney's Office, becoming the first woman ever to lead its criminal division. Upon recommendation and appointment from Senator Daniel Moynihan and President Bill Clinton respectively, in August 1994, Cote became a federal judge.