On 6 July 1553, at the age of 15, Edward VI died from a lung infection, possibly tuberculosis.[68] He did not want the crown to go to Mary because he feared she would restore Catholicism and undo his reforms, as well as those of Henry VIII, and so he planned to exclude her from the line of succession. His advisers, however, told him that he could not disinherit only one of his sisters, but that he would have to disinherit Elizabeth as well, even though she embraced the Church of England. Guided by John Dudley, 1st Duke of Northumberland, and perhaps others, Edward excluded both of his sisters from the line of succession in his will.[69] Contradicting the Succession Act, which restored Mary and Elizabeth to the line of succession, Edward named Dudley's daughter-in-law Lady Jane Grey, the granddaughter of Henry VIII's younger sister Mary, Queen of France, as his successor. Lady Jane's mother was Frances Brandon, who was Mary's cousin and goddaughter. Just before Edward VI's death, Mary was summoned to London to visit her dying brother. She was warned, however, that the summons was a pretext on which to capture her and thereby facilitate Lady Jane's accession to the throne.[70] Instead of heading to London from her residence at Hunsdon, Mary fled into East Anglia, where she owned extensive estates and Dudley had ruthlessly put down Kett's Rebellion. Many adherents to the Catholic faith, opponents of Dudley, lived there.[71] On 9 July, from Kenninghall, Norfolk, she wrote to the privy council with orders for her proclamation as Edward's successor.[72] On 10 July 1553, Lady Jane was proclaimed queen by Dudley and his supporters, and on the same day Mary's letter to the council arrived in London. By 12 July, Mary and her supporters had assembled a military force at Framlingham Castle, Suffolk.[73] Dudley's support collapsed, and Mary's grew.[74] Jane was deposed on 19 July.[75] She and Dudley were imprisoned in the Tower of London. Mary rode triumphantly into London on 3 August 1553 on a wave of popular support. She was accompanied by her half-sister Elizabeth, and a procession of over 800 nobles and gentlemen.[76] One of Mary's first actions as queen was to order the release of the Roman Catholic Duke of Norfolk and Stephen Gardiner from imprisonment in the Tower of London, as well as her kinsman Edward Courtenay.[77] Mary understood that the young Lady Jane was essentially a pawn in Dudley's scheme, and Dudley was the only conspirator of rank executed for high treason in the immediate aftermath of the coup. Lady Jane and her husband, Lord Guildford Dudley, though found guilty, were kept under guard in the Tower rather than executed, while Lady Jane's father, Henry Grey, 1st Duke of Suffolk, was released.[78] Mary was left in a difficult position, as almost all the Privy Counsellors had been implicated in the plot to put Lady Jane on the throne.[79] She appointed Gardiner to the council and made him both Bishop of Winchester and Lord Chancellor, offices he held until his death in November 1555. Susan Clarencieux became Mistress of the Robes.[80] On 1 October 1553, Gardiner formally crowned Mary at Westminster Abbey.[81]

At age 37, Mary turned her attention to finding a husband and producing an heir, thus preventing the Protestant Elizabeth (still her successor under the terms of Henry VIII's will and the Act of Succession of 1544) from succeeding to the throne. Edward Courtenay and Reginald Pole were both mentioned as prospective suitors, but her cousin Charles V suggested she marry his only son, Prince Philip of Spain.[82] Philip had a son from a previous marriage, and was heir apparent to vast territories in Continental Europe and the New World. As part of the marriage negotiations, a portrait of Philip by Titian was sent to her in September 1553.[83] Lord Chancellor Gardiner and the House of Commons unsuccessfully petitioned her to consider marrying an Englishman, fearing that England would be relegated to a dependency of the Habsburgs.[84] The marriage was unpopular with the English; Gardiner and his allies opposed it on the basis of patriotism, while Protestants were motivated by a fear of Catholicism.[85] When Mary insisted on marrying Philip, insurrections broke out. Thomas Wyatt the younger led a force from Kent to depose Mary in favour of Elizabeth, as part of a wider conspiracy now known as Wyatt's rebellion, which also involved the Duke of Suffolk, the father of Lady Jane.[86] Mary declared publicly that she would summon Parliament to discuss the marriage, and if Parliament decided that the marriage was not to the advantage of the kingdom, she would refrain from pursuing it.[87] On reaching London, Wyatt was defeated and captured. Wyatt, the Duke of Suffolk, his daughter Lady Jane, and her husband Guildford Dudley were executed. Courtenay, who was implicated in the plot, was imprisoned, and then exiled. Elizabeth, though protesting her innocence in the Wyatt affair, was imprisoned in the Tower of London for two months, then was put under house arrest at Woodstock Palace.[88]

After Philip's visit in 1557, Mary thought herself pregnant again with a baby due in March 1558.[144] She decreed in her will that her husband be the regent during the minority of her child.[145] However, no child was born, and Mary was forced to accept that Elizabeth was her lawful successor.[146] Mary was weak and ill from May 1558,[147] and died aged 42 at St. James's Palace during an influenza epidemic that also claimed the life of Reginald Pole later the same day, 17 November 1558. She was in pain, possibly from ovarian cysts or uterine cancer.[148] She was succeeded by her half-sister, who became Elizabeth I. Philip, who was in Brussels, wrote in a letter, "I felt a reasonable regret for her death."[149] Although her will stated that she wished to be buried next to her mother, Mary was interred in Westminster Abbey on 14 December in a tomb she would eventually share with Elizabeth. The Latin inscription on their tomb, Regno consortes et urna, hic obdormimus Elizabetha et Maria sorores, in spe resurrectionis (affixed there by James VI of Scotland when he succeeded Elizabeth as King James I of England) translates to "Consorts in realm and tomb, here we sleep, Elizabeth and Mary, sisters, in hope of resurrection".[150]