Möhler claimed the supreme chair of ecclesiastical history as a matter of course, and by right of seniority. He apologised for venturing to supersede one who had gained distinction in that lecture-room, but he hinted that he himself was the least fit of the two for dogmatics.

Ich habe mich für die historischen Fächer entschieden. Ihr Opfer, wenn Sie Dogmatik lesen, anerkenne ich, aber ich bitte das meinige nicht zu übersehen. Welcher Entschluss, ich möchte sagen, welche Unverschämtheit ist es, nach Ihnen und bei Ihren Lebzeiten, Kirchengeschichte in München zu doziren?

Döllinger took that branch for the time, but he never afterwards taught theology proper. As Möhler, who was essentially a theologian, deserted divinity to compose inferior treatises on the gnostics and the false decretals, Döllinger, by choice and vocation a divine, having religion as the purpose of his life, judged that the loftier function, the more spiritual service, was historical teaching. The problem is to know how it came to pass that a man who was eminently intelligent and perspicuous in the exposition of doctrines, but who, in narrative, description, and knowledge of character, was neither first nor second, resolved that his mission was history.

In early life he had picked up chance copies of Baronius and Petavius, the pillars of historic theology; but the motives of his choice lay deeper. Church history had long been the weakest point and the cause of weakness among the Catholics, and it was the rising strength of the German Protestants. Therefore it was the post of danger; and it gave to a theologian the command of a public of laymen. The restoration of history coincided with the euthanasia of metaphysic; when the foremost philosophic genius of the time led over to the historic treatment both of philosophy and religion, and Hamilton, Cousin, Comte, severally converted the science into its history. Many men better equipped for speculation than for erudition went the same way; the systematic theology was kept up in the universities by the influence of Rome, where scholasticism went on untouched by the romantic transformation. Writing of England, Wiseman said: "There is still a scholastic hardness in our controversial theology, an unbendingness of outward forms in our explanations of Catholic principles, which renders our theologians dry and unattractive to the most catholicly inclined portion of our Protestants." The choice which these youths made, towards 1830, was, though they did not know it, the beginning of a rift that widened.

Döllinger was more in earnest than others in regarding Christianity as history, and in pressing the affinity between catholic and historical thought. Systems were to him nearly as codes to Savigny, when he exhorted his contemporaries not to consolidate their law, lest, with their wisdom and knowledge, they should incorporate their delusions and their ignorance, and usurp for the state what belonged to the nation. He would send an inquiring student to the Historia Congregationis de Auxiliis and the Historia Pelagiana rather than to Molina or Lemos, and often gave the advice which, coming from Oriel, disconcerted Morris of Exeter: "I am afraid you will have to read the Jesuit Petavius." He dreaded the predominance of great names which stop the way, and everything that interposes the notions of an epoch, a region, or a school between the Church and the observer.

To an Innsbruck professor, lamenting that there was no philosophy which he could heartily adopt, he replied that philosophies do not subsist in order to be adopted. A Thomist or a Cartesian seemed to him as a captive, or a one-armed combatant. Prizing metaphysicians for the unstrung pearls which they drop beyond the seclusion of system, he loved the disjecta membra of Coleridge, and preferred the Pensieri, and Parerga und Paralipomena to the constructed work of Gioberti and Schopenhauer. He knew Leibniz chiefly in his letters, and was perceptibly affected by his law of continuous progression, his general optimism, and his eclectic art of extracting from men and books only the good that is in them; but of monadology or pre-established harmony there was not a trace. His colleague, Schelling, no friend to the friends of Baader, stood aloof. The elder Windischmann, whom he particularly esteemed, and who acted in Germany as the interpreter of De Maistre, had hailed Hegel as a pioneer of sound philosophy, with whom he agreed both in thought and word. Döllinger had no such condescension. Hegel remained, in his eyes, the strongest of all the enemies of religion, the guide of Tübingen in its aberrations, the reasoner whose abstract dialectics made a generation of clever men incapable of facing facts. He went on preferring former historians of dogma, who were untainted by the trail of pantheism, Baumgarten-Crusius, and even Muenscher, and by no means admitted that Baur was deeper than the early Jesuits and Oratorians, or gained more than he lost by constriction in the Hegelian coil. He took pleasure in pointing out that the best recent book on the penitential system, Kliefoth's fourth volume, owed its substance to Morinus. The dogmas of pantheistic history offended him too much to give them deep study, and he was ill prepared with counsel for a wanderer lost in the pervading haze. Hegelians said of him that he lacked the constructive unity of idea, and knew the way from effect to cause, but not from cause to law.

His own lectures on the philosophy of religion, which have left no deep furrow, have been praised by Ketteler, who was not an undiscriminating admirer. He sent on one of his pupils to Rosmini, and set another to begin metaphysics with Suarez; and when Lady Ashburton consulted him on the subject, he advised her to read Norris and Malebranche. He encouraged the study of remoter luminaries, such as Cusa and Raymundus, whose Natural Theology he preferred to the Analogy; and would not have men overlook some who are off the line, like Postel. But although he deemed it the mark of inferiority to neglect a grain of the gold of obsolete and eccentric writers, he always assigned to original speculation a subordinate place, as a good servant but a bad master, without the certainty and authority of history. What one of his English friends writes of a divine they both admired, might fitly be applied to him:

He was a disciple in the school of Bishop Butler, and had learned as a first principle to recognise the limitations of human knowledge, and the unphilosophical folly of trying to round off into finished and pretentious schemes our fragmentary yet certain notices of our own condition and of God's dealing with it.

He alarmed Archer Gurney by saying that all hope of an understanding is at an end, if logic be applied for the rectification of dogma, and to Dr. Plummer, who acknowledged him as the most capable of modern theologians and historians, he spoke of the hopelessness of trying to discover the meaning of terms used in definitions. To his archbishop he wrote that men may discuss the mysteries of faith to the last day without avail; "we stand here on the solid ground of history, evidence, and fact." Expressing his innermost thought, that religion exists to make men better, and that the ethical quality of dogma constitutes its value, he once said: "Tantum valet quantum ad corrigendum, purgandum, sanctificandum hominem confert." In theology as an intellectual exercise, beyond its action on the soul, he felt less interest, and those disputes most satisfied him which can be decided by appeal to the historian.

From his early reputation and his position at the outpost, confronting Protestant science, he was expected to make up his mind over a large area of unsettled thought and disputed fact, and to be provided with an opinion—a freehold opinion of his own—and a reasoned answer to every difficulty. People had a right to know what he knew about the end of the sixteenth chapter of St. Mark, and the beginning of the eighth chapter of St. John, the lives of St. Patrick and the sources of Erigena, the author of the Imitation and of the Twelve Articles, the Nag's Head and the Casket Letters. The suspense and poise of the mind, which is the pride and privilege of the unprofessional scholar, was forbidden him. Students could not wait for the master to complete his studies; they flocked for dry light of knowledge, for something defined and final, to their keen, grave, unemotional professor, who said sometimes more than he could be sure of, but who was not likely to abridge thought by oracular responses, or to give aphorism for argument. He accepted the necessity of the situation. A time came when everybody was invited, once a week, to put any imaginable question from the whole of Church history, and he at once replied. If this was a stimulus to exertion during the years spent in mastering and pondering the immense materials, it served less to promote originality and care than premature certitude and the craving for quick returns. Apart from the constant duty of teaching, his knowledge might not have been so extensive, but his views would have been less decided and therefore less liable to change.