Anyone who watched Rudolph W. Giuliani preside over ground zero in the days after 9/11 glimpsed elements of his strength: decisiveness, determination, self-confidence. Those qualities were also on display over the months he directed the cleanup of the collapsed World Trade Center. But today, with evidence that thousands of people who worked at ground zero have become sick, many regard Mr. Giuliani’s triumph of leadership as having come with a human cost. An examination of Mr. Giuliani’s handling of the extraordinary recovery operation during his last months in office shows that he seized control and largely limited the influence of...