But on Tuesday, that weapon had been disarmed.

“It has been my great privilege to serve as president and deeply rewarding to see SUNY Poly’s growth over the years,” Dr. Kaloyeros said in a brief resignation letter. “I am proud to have contributed to that. Now, however, I recognize that my continued leadership would pose a distraction from SUNY Poly continuing its good work.”

The complaint announced on Sept. 22 by Preet Bharara, the United States attorney in Manhattan, also resulted in charges against two of Mr. Cuomo’s former top aides: Joseph Percoco, who served as his executive deputy secretary and close confidant, and Todd R. Howe, whose relationship with Mr. Cuomo, a Democrat, dates back to the days his father, Mario M. Cuomo was governor.

But the complaint also offered an unflattering view of Mr. Cuomo’s preferred method of upstate development, which combined Dr. Kaloyeros’s vision of high-tech hubs in faded Erie Canal cities with the university’s ability to initiate large construction projects with less oversight than state agencies.

That included the so-called Buffalo Billion, which has poured hundreds of millions of dollars into that city, largely under the auspices of SUNY Poly. In the wake of Mr. Bharara’s complaint, Dr. Kaloyeros had already been suspended without pay, and Mr. Cuomo had already transferred authority for the Buffalo Billion to Empire State Development.

In remarks shortly after the arrest of Dr. Kaloyeros, Mr. Cuomo promised that the development agency’s leader, Howard Zemsky, would work “to learn from what happened.”