The individual who launched the “hardline” movement of Catholic Reformation was Pope Paul III (r. 1534 – 1549). Almost from the beginning of his rule, Paul was on the offensive: he commissioned a report in 1536 to evaluate the possibility and necessity of reform, which concluded that there were numerous abuses within the Church that had to be corrected (e.g. the lack of education of the clergy, the practice of earning incomes from parishes that bishops never visited, etc.), but there was no budging on doctrine. In other words, the essential beliefs and practices of the Church were judged to be entirely correct and Luther (and soon, Calvin) was judged to be entirely wrong.
In 1542 Paul III approved the creation of a permanent branch of the Church devoted to holding Protestantism in check: the Holy Office, better known as the Inquisition. The Inquisition existed to search out signs of heresy, including Protestantism, in areas under Catholic control. It had the right to subject people to interrogation and torture and in extreme cases, to execute them. The (in)famous Spanish branch of the Inquisition was under the control of the Spanish crown, but its methods and goals were essentially the same. Inquisitions had been around since the Middle Ages - the first one was in 1184 and targeted a heretical movement in southern France - but they had always been short-term responses to heresy. Under Paul III, the Inquisition became a permanent part of the Church.
The popes that followed Paul III were similar in their focus on re-emphasizing orthodoxy and creating institutions to combat heresy. Paul IV (r. 1555 – 1559) created the “Index” of forbidden books (in 1549) that would go on to form the basis of royal censorship in all Catholic countries for the next two centuries. He also enforced the stance of the Church that the Bible was not to be translated into vernacular languages but had instead to remain in Latin, an explicit rejection of the Protestant practice of translating the Bible into everyday language for Christians to read and interpret themselves. According to Catholic belief, reiterated under Paul IV, the Bible had to remain in Latin because only trained priests had the knowledge and authority to interpret it for laypeople. Laypeople, left to their own devices, would simply get the Bible’s message wrong and endanger their souls in the process.
Paul III, Paul IV, and the subsequent pope, Pius IV, all oversaw an ongoing series of meetings, the Council of Trent, that took place periodically between 1545 – 1563. There, Church officials debated all of the articles and charges that had been leveled against the Church, from the sale of indulgences, to the importance of good works in salvation, to the spiritual necessity of the sacraments. While it was initially organized to try to reconcile, at least in part, with Protestantism, hardliners within the Church won out in the subsequent debates and the Council reaffirmed almost all of the controversial parts of church doctrine and disputed articles of faith; the major exception was that the cardinals and bishops banned the sale of indulgences in the future (the Church still issued them, but they were no longer simply sold for cash). This was distressing to Emperor Charles V, who had earnestly hoped that the Church would give ground on some of the doctrinal issues and thereby win back Protestants in his lands; he even tried to prevent Pope Paul IV from taking office because the latter was so intransigent.
While the Council of Trent would not budge on doctrine, it did propose one monumental change to the Church: henceforth, priests would be formally trained for the job. After Trent, the Church organized and funded seminaries, colleges whose express purpose was the training of new priests. There, all priests would acquire a strong scholastic education (and, soon, most seminaries also included a humanistic education as well), fluency in Latin, and a deep understanding of the Bible and the writings of major Christian thinkers. The ad hoc nature of higher education for priests gave way to a formal and universal requirement: all priests would be well educated, not just those who had sought out a university themselves. While abuses of power and moral laxness were not eliminated from the Church, the one definitive change for the better in terms of the experience of lay Catholics was that their priests were now supposed to be experts in Christian theology.