In 1811, Shelley anonymously published a pamphlet called 'The Necessity of Atheism' which was brought to the attention of the university administration and he was called to appear before the Oxford College's fellows, including the Dean, George Rowley. His refusal to repudiate the authorship of the pamphlet resulted in his expulsion from Oxford on 25 March 1811, along with Hogg. The rediscovery in mid-2006 of Shelley's long-lost 'Poetical Essay on the Existing State of Things' — a long, strident anti-monarchical and anti-war poem printed in 1811 in London by Crosby and Company as "by a gentleman of the University of Oxford" and dedicated to Harriet Westbrook — gives a new dimension to the expulsion, reinforcing Hogg's implication of political motives ("an affair of party"). Shelley was given the choice to be reinstated after his father intervened, on the condition that he would have to recant his avowed views. His refusal to do so led to a falling-out with his father.
Four months after being expelled from Oxford, on 28 August 1811, the 19-year-old Shelley eloped to Scotland with the 16-year-old Harriet Westbrook, a pupil at the same boarding school as Shelley's sisters, whom his father had forbidden him to see. Harriet Westbrook had been writing Shelley passionate letters threatening to kill herself because of her unhappiness at the school and at home. Shelley, heartbroken after the failure of his romance with his cousin, Harriet Grove, cut off from his mother and sisters, and convinced he had not long to live, impulsively decided to rescue Harriet Westbrook and make her his beneficiary. Harriet Westbrook's 28-year-old sister Eliza, to whom Harriet was very close, appears to have encouraged the young girl's infatuation with the future baronet. The Westbrooks pretended to disapprove but secretly encouraged the elopement. Sir Timothy Shelley, however, outraged that his son had married beneath him (Harriet's father, though prosperous, had kept a tavern) revoked Shelley's allowance and refused ever to receive the couple at Field Place. Shelley invited his friend Hogg to share his ménage but asked him to leave when Hogg made advances to Harriet. Harriet also insisted that her sister Eliza, whom Shelley detested, live with them. Shelley was also at this time increasingly involved in an intense platonic relationship with Elizabeth Hitchener, a 28-year-old unmarried schoolteacher of advanced views, with whom he had been corresponding. Hitchener, whom Shelley called the "sister of my soul" and "my second self", became his muse and confidante in the writing of his philosophical poem Queen Mab, a Utopian allegory.
During this period, Shelley travelled to Keswick in England's Lake District, where he visited the poet Robert Southey, under the mistaken impression that Southey was still a political radical. Southey, who had himself been expelled from the Westminster School for opposing flogging, was taken with Shelley and predicted great things for him as a poet. He also informed Shelley that William Godwin, author of 'Political Justice', which had greatly influenced him in his youth, and which Shelley also admired, was still alive. Shelley wrote to Godwin, offering himself as his devoted disciple and informing Godwin that he was "the son of a man of fortune in Sussex" and "heir by entail to an estate of 6,000 £ per an." Godwin, who supported a large family and was chronically penniless, immediately saw in Shelley a source of his financial salvation. He wrote asking for more particulars about Shelley's income and began advising him to reconcile with Sir Timothy. Meanwhile, Sir Timothy's patron, the Duke of Norfolk, a former Catholic who favoured Catholic Emancipation, was also vainly trying to reconcile Sir Timothy and his son, whose political career the Duke wished to encourage. A maternal uncle ultimately supplied money to pay Shelley's debts, but Shelley's relationship with the Duke may have influenced his decision to travel to Ireland. In Dublin, Shelley published his 'Address to the Irish People', priced at fivepence, "the lowest possible price" to "awaken in the minds of the Irish poor a knowledge of their real state, summarily pointing out the evils of that state and suggesting a rational means of remedy – Catholic Emancipation and a repeal of the Union Act" (the latter "the most successful engine that England ever wielded over the misery of fallen Ireland"). His activities earned him the unfavourable attention of the British government.
Shelley was increasingly unhappy in his marriage to Harriet and particularly resented the influence of her older sister Eliza, who discouraged Harriet from breastfeeding their baby daughter (Elizabeth Ianthe Shelley [1813-76]). Shelley accused Harriet of having married him for his money. Craving more intellectual female companionship, he began spending more time away from home, among other things, studying Italian with Cornelia Turner and visiting the home and bookshop of William Godwin. Eliza and Harriet moved back with their parents.
Shelley's mentor Godwin had three highly educated daughters, two of whom, Fanny Imlay and Claire Clairmont, were his adopted step-daughters. Godwin's first wife, the celebrated feminist Mary Wollstonecraft, author of 'A Vindication of the Rights of Woman', had died giving birth to Godwin's biological daughter Mary Wollstonecraft Godwin, named after her mother. The brilliant Mary was being educated in Scotland when Shelley first became acquainted with the Godwin family. When she returned Shelley fell madly in love with her, repeatedly threatening to commit suicide if she didn't return his affections.
On 28 July 1814, Shelley abandoned Harriet, now pregnant with their son Charles (November 1814 – 1826) and (in imitation of the hero of one of Godwin's novels) he ran away to Switzerland with Mary and her stepsister Claire Clairmont (also 16). The three sailed to Europe, and made their way across France to Switzerland on foot, reading aloud from the works of Rousseau, Shakespeare and Mary Wollstonecraft.
After six weeks, homesick and destitute, the three young people returned to England. The enraged William Godwin refused to see them, though he still demanded money, to be given to him under another name, to avoid scandal.
On 10 December 1816, the body of Shelley's estranged wife Harriet was found in an advanced state of pregnancy, drowned in the Serpentine in Hyde Park, London. Shelley had made generous provision for Harriet and their children in his will and had paid her a monthly allowance as had her father. It is thought that Harriet, who had left her children with her sister Eliza and had been living alone under the name of Harriet Smith, mistakenly believed herself to have been abandoned by her new lover, 36-year-old Lieutenant Colonel Christopher Maxwell, who had been deployed abroad, after a landlady refused to forward his letters to her. On 30 December 1816, barely three weeks after Harriet's body was recovered, Shelley and Mary Godwin were married. The marriage was intended partly to help secure Shelley's custody of his children by Harriet and partly to placate Godwin, who had coldly refused to speak to his daughter for two years, and who now received the couple. The courts, however, awarded custody of Shelley and Harriet's children to foster parents, on the grounds that Shelley was an atheist.