On the morning of Thursday, July 31, James B. Milliken was enjoying a round of golf at the remote Sand Hills club in Western Nebraska when his cellphone buzzed.

Milliken was still days away from taking the helm of the sprawling University of California system, but his new office was on the line with disturbing news: The Trump administration was freezing hundreds of millions of dollars of research funding at the University of California, Los Angeles, UC’s biggest campus. Milliken quickly packed up and made the five-hour drive to Denver to catch the next flight to California.

He landed on the front lines of one of the most confounding cultural battles waged by the Trump administration.

The grant freeze was the latest salvo in the administration’s broader campaign against elite universities, which it has pilloried as purveyors of antisemitism and “woke” indoctrination. Over the next four months, the Justice Department targeted UCLA with its full playbook for bringing colleges to heel, threatening it with multiple discrimination lawsuits, demanding more than $1 billion in fines and pressing for a raft of changes on the conservative wish list for overhauling higher education.

In the months since Milliken’s aborted golf game, much has been written about the Trump administration’s efforts to impose its will on UCLA, part of the nation’s largest and most prestigious public university system. But an investigation by ProPublica and The Chronicle of Higher Education, based on previously unreported documents and interviews with dozens of people involved, reveals the extent to which the government violated legal and procedural norms to gin up its case against the school. It also surfaced something equally alarming: How the UC system’s deep dependence on federal money inhibited its willingness to resist the legally shaky onslaught, a vulnerability the Trump administration’s tactics brought into sharp focus.