The Church courts not only had jurisdiction over the whole clerical order, but exercised wide powers even over the laity. To them alone belonged the right to enforce spiritual penalties, to deal with cases of oaths, promises, anything in which a man's faith was pledged; to decide as to the property of intestates, to pronounce in every case of inheritance whether the heir was legitimate, to declare the law as to wills and marriage. Administering as they did an enlightened system of law, they profited by the new prosperity of the country, and the judicial and pecuniary disputes which came to them had never been so abundant as now. Henry was keenly alive to the fact that the archdeacons' courts now levied every year by their fines more money than the whole revenue of the crown. Young archdeacons were sent abroad to be taught the Roman law, and returned to preside over the newly-established archdeacons' courts; clergy who sought high office were bound to study before all things, even before theology, the civil and canon law. The new rules, however, were as yet incomplete and imperfectly understood in England; the Church courts were without the power to put them in force; the procedure was hurried and irregular; the judges were often ill-trained, and unfit to deal with the mass of legal business which was suddenly thrown on them; the ecclesiastical authorities themselves shrank from defiling the priesthood by contact with all this legal and secular business, and kept the archdeacons in deacons' orders; the more religious clergy questioned whether for an archdeacon salvation were possible. In the eight years of Henry's rule one hundred murders had been committed by clerks who had escaped all punishment save the light sentences of fine and imprisonment inflicted by their own courts, and Henry bitterly complained that a reader or an acolyte might slay a man, however illustrious, and suffer nothing save the loss of his orders.

Since the beginning of Henry's reign, too, there had been an enormous increase of appeals to Rome. Questions quite apart from faith or morals, and that mostly concerned property, were referred for decision to a foreign court. The great monasteries were exempted from episcopal control and placed directly under the Pope; they adopted the customs and laws which found favour at Rome; they upheld the system of appeals, in which their wealth and influence gave them formidable advantages. The English Church was no longer as in earlier times distinct from the rest of Christendom, but was brought directly under Roman influence. The clergy were more and more separated from their lay fellow citizens; their rights and duties were determined on different principles; they were governed by their own officers and judged by their own laws, and tried in their own courts; they looked for their supreme tribunal of appeal not to the King's Court, but to Rome; they became, in fact, practically freed from the common law.

No king, and Henry least of all, could watch unmoved the first great body which threatened to stand wholly outside the law of the land; and the ecclesiastical pretensions of the time were perhaps well matched by the pretensions of the State. The king had prepared for the coming conflict by a characteristic act of high-handed imperiousness in the election of the chancellor-archbishop to carry out his policy. But all such schemes of imperative despotism were vain. No sooner was Thomas consecrated than it became plain that his ecclesiastical training would carry the day against the influence of Henry. As rapidly as he had "thrown off the deacon" to become the chancellor, so he now went through the sharper change of throwing off the chancellor to become the archbishop. With keen political sagacity he at once sought the moral support of the religious party who had so vehemently condemned his appointment. The gorgeous ostentation of his old life gave way to an equally elaborate scheme of saintliness. He threw away with tears his splendid dress to put on sackcloth and the black cloak of the monk. His table was still covered with gold and silver dishes and with costly meats, but the hall was now crowded with the poor and needy, and at his own side sat only the most learned and holy among the monks and clergy. Forty clerks "most learned in the law" formed his household. He visited the sick in the infirmary, and washed the feet of thirteen poor men daily. He sat in the cloister like one of the monks, studying the canon law and the Holy Scriptures. He joined their prayers in the Church and took part in their secret councils. The monks who had suffered under the heavy hand of Theobald, when their dainty foods were curtailed and their cherished privileges sharply denied them, hailed joyfully the unexpected attitude of their new master. "This is the finger of God," men said, "this, indeed, is the work of the right hand of the Most High." "As he had been accustomed to the pre-eminence over others in worldly glory," commented another observer, "so now he determined to be the foremost in holy living."

Rumours spread that there were to be other changes besides that of "holy living." The see of Canterbury under the new primate was to win back all lands and privileges lost during the civil wars, at whatever cost to the interests of the whole court party, of barons who found their rights to Church appointments and Church lands questioned, and of clerks of the royal household who trembled for their posts and benefices. There was soon no lack of enemies at court, old and new, ready to carry to Henry whispers that would appeal most subtly to his fears,—whispers that the royal dignity itself was in danger; that he must look to himself and his heirs, or the story of Stephen's time would be told over again, and that man alone would in future be king, whom the clergy should elect and the archbishop approve. Henry's bitter anger was aroused when Thomas resigned the chancellorship, "not now wishing to be in the royal court, but desiring to have leisure for prayers, and to superintend the business of the Church." The king retorted by forcing Thomas to resign his archdeaconry with its rich fees; and at his landing in January 1163 he received the archbishop, who came to meet him, "with averted face." Thomas, on his part, added another grievance by refusing on ecclesiastical grounds to allow Henry to marry his brother to Stephen's daughter-in-law, the Countess of Warenne; and on the general question of the relations of Church and State, he hastened to define his views with sharp precision in an eloquent sermon preached before the king. "Henry observing it word by word, and understanding from it how greatly Thomas put the ecclesiastical before the civil right, did not receive this doctrine with an equal mind, for he perceived that the archbishop was far from his own view, that the Church had neither rights nor possessions save by his favour." The attitude of Thomas was yet further strengthened and defined when, in May 1163, he went to attend a great Council held at Tours, where he was brought more immediately under the influence of the ecclesiastical movement of the day. There he sought, with a meaning that Henry must clearly have understood, to procure the canonization of Anselm from Pope Alexander, who, however, was far too politic amid his own difficulties, and in his need for Henry's help, to commit himself either by consent or by refusal.

The inevitable controversy declared itself soon after the return of Thomas from Tours. Throughout July and August one question after another was hurried forward for settlement between king and primate. On July 1 the king proposed a change in the collection of the land tax, which would have increased the royal revenues at the expense of the revenues of the shire. Since the Conquest there had never been a single instance of an attempt to resist the royal will in matters of finance, but Thomas showed no hesitation. He flatly refused consent to an arbitrary act of this kind. He made no objection to the payment of the tax, but he was determined to prevent the local revenues being seized in this way by the king. His action seems to have been wise and patriotic, and his triumph was complete. Henry was forced to abandon the scheme. Having awakened the anger of the king, Thomas next alienated the whole party of the barons by pressing his demands for the recovery of lands belonging to his see. Tunbridge, Rochester, now in the custody of the crown itself, Hythe, Saltwood, and a number of other manors became the subjects of sharp contention. The archbishop urged a doubtful claim, which he had inherited from Theobald, to appoint the priest to a church on the land of William of Eynesford, a tenant of the king. William resisted, and Thomas made his first false move by excommunicating him. Henry at once appealed to the "customs" of the kingdom, which forbade such sentence on the king's barons without the royal consent, and Thomas had to withdraw his excommunication. "I owe him no thanks for it!" cried the angry king.

A more serious strife was raised when Thomas came into direct collision with Henry on the inevitable question of the punishment of clerks for crime against the common law. If the king was determined to bring about a fundamental reform in the administration of justice, the Primate was equally resolute that as archbishop he would have nothing to do with reforms which he might have countenanced as chancellor. He prudently sought at first to divert attention from the real issue by increasing the severity of judgments in the ecclesiastical courts. A clerk had stolen a chalice; he insisted on his trial in the Church Court, but to appease the king ordered him to be branded,—a punishment condemned by ecclesiastical law which considered all injury to the person as defiling the image of God. Such devices, however, were thrown away on Henry. When another clerk, Philip de Broc, who had been accused of manslaughter, was set free by the Church courts, the king's justiciar ordered him to be brought to a second trial before a lay judge. Philip refused to submit. The justiciar then charged him with contempt of court for his vehement and abusive language to the officer who summoned him, but the archbishop demanded that for this charge, too, he should be tried by ecclesiastical law. Henry was forced to content himself with sending a detachment of bishops and clergy to watch the trial. They returned with the news that the court had refused to reconsider the charge of manslaughter, and had merely condemned Philip for insolence; he was ordered to make personal satisfaction to the sheriff, standing (clerk as he was) naked before him, and submitting to a heavy fine; his prebend was to be forfeited to the king for two years; for those two years he was to be exiled and his movable goods were confiscated.

The punishment might seem severe enough, but Henry would accept no compromise. With a burst of fury he declared that just judgment for murder was refused because the offender was in orders. Resolute that the question should once for all be settled, he summoned a council at Westminster on October 1. There he demanded, "for love of him and for safety of the kingdom," that accused clerks should be tried by the common law, and that if proved guilty, they should be degraded by the bishops, and given up to the executioner for punishment. He complained of the exactions of the ecclesiastical courts, and urged that in all matters concerning these courts or the rights of the clergy, the bishops should return to the customs of Henry the First. Such a course would have left them at the king's mercy, and the prelates wavered in their sore distress. The king's friends contended that a guilty clerk deserved punishment double that of a layman, and urged the need of submission at this moment when the Church was torn asunder by schism; and the bishops frankly admitted a yet more pressing consideration: "For if we do not what the king wishes," they said, "flight will be cut off from us, and no man will seek after our souls; but if we consent to the king, we shall own the sanctuary of God in heredity, and shall sleep safely in the possession of our churches." On the other hand, the archbishop had no mind to resign without a contest all the results of the great tide of feeling which had swept the Church onward far past its old landmarks. For him there was no going back to a traditional past from which the Church had shaken itself free, and in which, though king and barons might see the freedom of the State, he saw the enslaving and degradation of the clergy. He vehemently asserted that the "customs" of the Church were of greater authority than any "customs" of the kingdom, that its canon law claimed obedience as against all traditional national law whatever; and with keen political insight he insisted on the dangers that would follow if once they allowed the charm of prescription to be broken, or the ecclesiastical liberties to be touched. He boldly led the way in his answer to the king: "We will obey in all things saving our order;" and as the bishops were asked one by one, they took courage to follow, and "one voice was in the mouth of all of them." Such a phrase had never been heard in England before, and Henry, with ready indignation, at once demanded the withdrawal of the words. When Thomas refused, he broke up the council in a burst of anger, and suddenly rode away from London, instantly followed by the whole body of trembling bishops, who hurried after him in abject terror, "lest before they should be able to catch him up, they should already have lost their sees." Thomas was left alone—"there was not one who would know him,"—while the prelates, coming up in time with their terrible lord, agreed henceforth to guide their words by his good pleasure.

From this moment all the elements of strife were prepared, and there was but outer show of harmony when king and archbishop, a few days later, joined at Westminster to celebrate with solemn pomp the translation of the remains of the sainted Confessor. In declaring war upon local jurisdictions, whether of clergy, or nobles, or burghers, or independent shire courts, Henry was defying all the traditions and convictions of his age,—an age when local feeling was a force which we are now quite unable to measure. The nobles, the guilds, and the rising towns had already won long before, or were now seeking to win as their most cherished privilege, the right to their own justice without interference from any higher power. They naturally looked with sympathy on the rights exercised by the clergy within their own body; they felt that whatever had been won by one class might later be won by another, and that liberties which were enjoyed by so enormous a body as the clerical order were a benefit in which the whole people had a share. If the king was determined to wage war on "privilege," clergy and people were equally resolute to defend "liberty." Moreover, in attacking the special jurisdiction of the Church, Henry had to encounter a force to which there is no parallel in our own time. An English king had doubtless less to fear from the Church than had any continental ruler. Abroad the bishop-stool, the abbey, the Church, were oases in the midst of perpetual war,—the only spots where peace and law and justice spoke in protest against the chaos of the world. But England was, in comparison with the rest of the western world, a country of peace and law. There the Church was less powerful against the State because the State had never handed over its duty of maintaining justice and law and right to the exclusive guardianship of the Church. None the less it was a formidable matter to rouse the hostility of a body which included not only all the religious world, but all the educated classes, and penetrated even to the despised villeinage and the poor freemen whose sons pressed into its lower ranks. The Church with which Henry had to deal was no longer the same that the Conqueror had easily bent to his will. It had received its training and felt its strength in political action; it had developed a close corporate spirit; it had an admirable organization; it possessed the most advanced as well as the most merciful legal system of the age. Its courts had strong claims to popular regard. Their punishments were more merciful than the savage sentences of the lay courts; and they held out great advantages to the rich, since the penances they inflicted could be commuted for money. Their system of law, moreover, was far in advance of the barbarous rules of customary law; and they were backed by all the authority of the Roman Curia and of the religious feeling of the day.

Henry had, however, peculiar advantages in the contest. He was master of a disciplined body of ministers and servants, in whom he could confidently trust. He was sure, in this matter at least, of the support of the lay baronage, who had long arrears of jealousy to make up against their hereditary opponents the clergy, and who were not likely now to forget that no party in the Church had ever made common cause with the feudal lords. He could count on the obedience of the secular clergy. In France or Germany the bishops were members of the great houses, and as powerful local rulers wielded a vast feudal authority. In England their position was very different. They were drawn from the staff of the king's chapel, and had their whole training in the administration of the court; and they formed an official nobility who were charged, in common with the secular nobility, with the conduct of the general business of the realm. They were appointed to their places by the king for services done to him, and as instruments of his policy. Neither Pope nor people had any share in their election. Their estates were granted them by the same titles, and with the same obligations as those of feudal barons; the king could withhold their temporalities, sequestrate their lands, confiscate their personal goods, and burden them with heavy fines; they lay absolutely at his mercy without appeal. Every tie of feudal duty, of official training, of prudent self-interest, forced them into subjection to the Crown. Their Roman sympathies were quenched as they watched the growing independence of the monasteries, and saw Church endowments taken to enrich the new religious houses of every kind which were springing up all over England. They feared the new authority claimed by legates, which threatened to withdraw the clergy, if they chose to assert their claims, from regular episcopal jurisdiction. They were thrown on the side of the king in ecclesiastical questions, drawn together by a common cause, both alike found their interest in the defence of national tradition as opposed to foreign custom.

Their leaders too looked coldly on the cause of the Primate. The Archbishop of York, Roger of Pont l'Evêque, once the companion of Thomas in Theobald's household, was now his personal enemy and rival. The two prelates inherited the secular strife as to which see should have the precedence. Moreover, while Canterbury represented the papal policy and always looked to Rome, York preserved some faint traditional leanings towards the liberties of the Irish and Scotch churches from whence the Christianity of the north had sprung. The Bishop of London, Gilbert Foliot, who, with the approval of Thomas, had been translated from Hereford only five months before, was, by his mere position, marked out as the chief antagonist of the archbishop, for St Pauls was at the head of the whole body of secular clergy throughout southern England, and to its bishop inevitably fell the leadership of this party against Canterbury, which was in the hands of a monastic chapter. The Bishop of Winchester, Henry of Blois, could well remember the struggle between Church and Crown under a far weaker king twenty six years before, when the bishops had wisely withdrawn from a contest where they had "seen swords unsheathed and knew it was no longer a joking matter, but a struggle of life and death," and with the prudence born of long political experience he was for moderate counsels. The Bishop of Chichester, Hilary, doubtless remembered the inconvenient part which Thomas as chancellor had played in his own trial a few years before, and might gladly recognize a poetic justice in seeing Thomas's old doctrines of the supremacy of the State now applied to himself. "Every plant," he once said with taunting reference to the king's part in Thomas's election, "which my heavenly Father has not planted shall be rooted up." Thomas bitterly added another verse as he heard of the saying, "This man had among the brethren the place of Judas the traitor." There seems to have been a general impression that the position of the Primate was extremely critical, and he was besieged by advisers who urged submission, by messengers from pope and cardinals, by panic-stricken churchmen. Beset on all sides the Primate wavered, and at last promised to swear obedience to the "customs of the kingdom." Immediately the king summoned prelates and barons to witness his submission, and the famous Council of Clarendon met for this purpose in 1164.