Born within earshot of Bow bells, and venerated for centuries as the "light of London", Thomas Becket was the most celebrated medieval Englishman (if the French-speaking son of an immigrant Norman businessman can be described straightforwardly as "English"). His brutal murder  that of an archbishop in his own cathedral  shook 12th-century Europe to its roots. The murder was reported in minute detail: no fewer than five of Becket's companions in Canterbury cathedral on that fateful day, 29 December 1170, wrote eye-witness accounts. Becket was not an obvious candidate for sanctity: even his supporters knew him to be proud, fond of hunting, extravagant and showy. David Knowles pointed out years ago that, though many of his contemporaries admired Becket, nobody but the king who killed him claimed to have loved him.

But it was the fact of his death, not the manner of his life, that mattered to Becket's contemporaries. The age of the martyrs was long past: but now, beyond expectation, the blood of a priest, spilled in defence of the holy church, offered a potent new symbol and a source of miracle and blessing. Cures began at Becket's grave as soon as the desecrated cathedral had been cleansed and reopened. Pope Alexander III canonised him on Ash Wednesday 1173, and in July the following year King Henry II, in need of heavenly support against multiple revolts in France and England, came barefoot to the tomb of his enemy, confessed the careless words that had prompted the assassins, and submitted to a token scourging by a hundred very nervous Canterbury monks. Images of Becket multiplied, chips of his bones and drops of his blood were cherished as relics from southern Sicily to the shores of the Baltic, and his life and death were chronicled in Latin hymns and Icelandic sagas. For four centuries pilgrims would flock in their tens of thousands from every corner of the Christian world to seek the intercession of Chaucer's "holy, blissful martyr".

It is not hard to see why Becket's cult had so powerful an appeal. For more than a century zealous popes and bishops had laboured to extricate the church from its immemorial subjugation to kings and barons. They resisted royal interference in clerical appointments, lay misappropriation of church lands and revenues, and legal restrictions on communication between the pope and local churches. In England, the saintly Archbishop Anselm had confronted Henry I over these ideals, and Becket witnessed similar struggles at first hand as a clerk in the service of the gentle but shrewd Archbishop Theobald. It was Theobald who persuaded Henry II to make Becket lord chancellor, confident that this charismatic administrator could be trusted to restrain a rapacious young king, and protect the church's rights.

He was to be bitterly disappointed, for as chancellor Becket threw himself unequivocally behind Henry. They became inseparable companions, and Becket did all he could to extend royal income and influence at the church's expense. So when Theobald died in 1161, Henry, confident of Becket's loyalty, passed over older and better qualified men such as Gilbert Foliot, bishop of Hereford, and made Becket archbishop, for which he earned the new primate Foliot's undying enmity.

But if Henry had hoped that Becket would now administer church as well as state on his behalf, it was his turn to be disappointed. Within weeks Becket resigned as chancellor and made it clear that now he was the church's man. Flamboyant even in his piety, he took to wearing a hair shirt under his robes, immersed himself in penitential cold baths and washed the feet of 30 paupers each day before he dined.

Inevitably he soon came eyeball to eyeball with Henry. There were many causes for the mounting enmity between the two former friends, but they included the exemption of clergy from the jurisdiction of the secular courts. Delinquent clerics were to be tried, Becket insisted, by ecclesiastical courts, not the king's judges, even for crimes such as murder or theft. Since the church courts did not inflict the death penalty, this was no small matter.

Today's readers, all too conscious of ecclesiastical cover-up of clerical abuse, are unlikely to warm to Becket's cause, but more was at stake than clerical privilege. The medieval church was the sole source of moral value, and one of the few contexts within which criticism of tyrannical rule was possible. Kings such as Henry II were rarely concerned with abstract justice, and royal control of the church posed problems not unlike those posed nowadays by state censorship of the press or suppression of the right of peaceful protest. Becket saw himself as a champion of the cause of Christ and the liberties of the church. But he was never a team player, not all his fellow bishops shared what they saw as his extremist views, and many of those who did were too timid to stand against the most powerful king in Europe. From 1164 an isolated Becket spent six frustrating years in exile, living as a monk in France, till a patched-up reconciliation with Henry enabled his return to Canterbury, just months before his murder.

Becket had no illusions about his long-term safety. Henry repeatedly and ominously refused to exchange the kiss of peace with him, and the archbishop knew his stand against royal demands was likely to end badly. His enemies thought him a charlatan who deliberately courted death. He himself believed his stand was essential to vindicate the universal church's freedoms, and events were to prove him right, for his martyrdom became the emblem of spiritual resistance to secular tyranny. No king till Henry VIII dared repeat Henry II's assault on ecclesiastical jurisdiction. Four centuries on, when the Tudor Henry finally assumed total control of the church, he symbolised the reversal of Becket's victory by denouncing him as a traitor, burning his bones, and outlawing even the mention of his name, a verdict endorsed by protestant and secular historians till modern times.

John Guy is one of our most distinguished Tudor historians and therefore an unexpectedly sympathetic biographer of Becket, though his earlier books include important studies of More and Wolsey  other chancellors called Thomas who fell foul of a tyrannical King Henry. He discounts the unanimous claim of Becket's biographers that, even as a student in Paris, he had preserved his chastity, but Guy admires Becket's flair, courage and integrity, and he despises his royal opponent as a fickle, unscrupulous and vengeful opportunist.

His book does not drastically alter the picture of Becket offered by specialist studies, such as Anne Duggan's splendid 2004 volume in the "Reputations" series, but Guy is more interested in Becket's elusive psychology than in the ideals that he saw himself as defending, and this study is accordingly stronger on particulars than on principles. So on Guy's account, Becket died for the prerogatives of the See of Canterbury rather than the freedom of the universal church. But he has given us an unfailingly lively, accessible and vividly written portrait of one of the giants of the middle ages.

 Eamon Duffy's Saints, Sacrilege and Sedition is published by Bloomsbury on 31 May.