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Governor-General

The Radcliffe Commission, dividing Bengal and Punjab, completed its work and reported to Mountbatten on 12 August; the last Viceroy held the maps until the 17th, not wanting to spoil the independence celebrations in both nations. There had already been ethnically charged violence and movement of populations; publication of the Radcliffe Line dividing the new nations sparked mass migration, murder, and ethnic cleansing. Many on the "wrong side" of the lines fled or were murdered, or murdered others, hoping to make facts on the ground which would reverse the commission's verdict. Radcliffe wrote in his report that he knew that neither side would be happy with his award; he declined his fee for the work. Christopher Beaumont, Radcliffe's private secretary, later wrote that Mountbatten "must take the blame—though not the sole blame—for the massacres in the Punjab in which between 500,000 to a million men, women and children perished". Jinnah did what he could for the eight million people who migrated to Pakistan; although by now over 70 and frail from lung ailments, he travelled across West Pakistan and personally supervised the provision of aid. According to Ahmed, "What Pakistan needed desperately in those early months was a symbol of the state, one that would unify people and give them the courage and resolve to succeed."

Among the restive regions of the new nation was the North-West Frontier Province. The referendum there in July 1947 had been tainted by low turnout as less than 10 per cent of the population were allowed to vote. On 22 August 1947, just after a week of becoming governor general, Jinnah dissolved the elected government of Khan Abdul Jabbar Khan. Later on, Abdul Qayyum Khan was put in place by Jinnah in the Pashtun -dominated province despite him being a Kashmiri. On 12 August 1948 the Babrra massacre in Charsadda occurred resulting in the death of 400 people aligned with the Khudai Khidmatgar movement.

Along with Liaquat and Abdur Rab Nishtar, Jinnah represented Pakistan's interests in the Division Council to appropriately divide public assets between India and Pakistan. Pakistan was supposed to receive one-sixth of the pre-independence government's assets, carefully divided by agreement, even specifying how many sheets of paper each side would receive. The new Indian state, however, was slow to deliver, hoping for the collapse of the nascent Pakistani government, and reunion. Few members of the Indian Civil Service and the Indian Police Service had chosen Pakistan, resulting in staff shortages. Partition meant that for some farmers, the markets to sell their crops were on the other side of an international border. There were shortages of machinery, not all of which was made in Pakistan. In addition to the massive refugee problem, the new government sought to save abandoned crops, establish security in a chaotic situation, and provide basic services. According to economist Yasmeen Niaz Mohiuddin in her study of Pakistan, "although Pakistan was born in bloodshed and turmoil, it survived in the initial and difficult months after partition only because of the tremendous sacrifices made by its people and the selfless efforts of its great leader."

The princely states of India were advised by the departing British to choose whether to join Pakistan or India. Most did so prior to independence, but the holdouts contributed to what have become lasting divisions between the two nations. Indian leaders were angered at Jinnah's attempts to convince the princes of Jodhpur, Udaipur, Bhopal and Indore to accede to Pakistan—the latter three princely states did not border Pakistan. Jodhpur bordered it and had both a Hindu majority population and a Hindu ruler. The coastal princely state of Junagadh, which had a majority-Hindu population, did accede to Pakistan in September 1947, with its ruler's dewan, Sir Shah Nawaz Bhutto, personally delivering the accession papers to Jinnah. But two of three vassal states that were subject to the suzerainty of Junagadh— Mangrol and Babariawad —declared their independence from Junagadh and acceded to India. In response, the Nawab of Junagarh militarily occupied the two states. Subsequently, the Indian Army occupied the principality in November, forcing its former leaders, including Bhutto, to flee to Pakistan, beginning the politically influential Bhutto family.

The most contentious of the disputes was, and continues to be, that over the princely state of Kashmir. It had a Muslim-majority population and a Hindu maharaja, Sir Hari Singh, who stalled his decision on which nation to join. With the population in revolt in October 1947, aided by Pakistani irregulars, the maharaja acceded to India; Indian troops were airlifted in. Jinnah objected to this action, and ordered that Pakistani troops move into Kashmir. The Pakistani Army was still commanded by British officers, and the commanding officer, General Sir Douglas Gracey, refused the order, stating that he would not move into what he considered the territory of another nation without approval from higher authority, which was not forthcoming. Jinnah withdrew the order. This did not stop the violence there, which broke into the First India–Pakistan War.

Some historians allege that Jinnah's courting the rulers of Hindu-majority states and his gambit with Junagadh are evidence of ill-intent towards India, as Jinnah had promoted separation by religion, yet tried to gain the accession of Hindu-majority states. In his book Patel: A Life, Rajmohan Gandhi asserts that Jinnah hoped for a plebiscite in Junagadh, knowing Pakistan would lose, in the hope the principle would be established for Kashmir. However, when Mountbatten proposed to Jinnah that, in all the princely States where the ruler did not accede to a Dominion corresponding to the majority population (which would have included Junagadh, Hyderabad and Kashmir), the accession should be decided by an 'impartial reference to the will of the people', Jinnah rejected the offer. Despite the United Nations Security Council Resolution 47, issued at India's request for a plebiscite in Kashmir after the withdrawal of Pakistani forces, this has never occurred. In January 1948, the Indian government finally agreed to pay Pakistan its share of British India's assets on 15 January 1948. The partition violence stopped by 18 January following the fast by Mahatma Gandhi with religious rioters promising Gandhi to frown upon the violence. Only days later, on 30 January, Gandhi was assassinated by Nathuram Godse, a Hindutva activist, who claimed that Gandhi was pro-Muslim. After hearing about Gandhi's murder, Jinnah publicly made a brief statement of condolence, calling Gandhi "one of the greatest men produced by the Hindu community". In February 1948, in a radio talk broadcast addressed to the people of the US, Jinnah expressed his views regarding Pakistan's constitution to be in the following way:

The Constitution of Pakistan is yet to be framed by the Pakistan Constituent Assembly, I do not know what the ultimate shape of the constitution is going to be, but I am sure that it will be of a democratic type, embodying the essential principles of Islam. Today these are as applicable in actual life as these were 1300 years ago. Islam and its idealism have taught us democracy. It has taught equality of man, justice and fair play to everybody. We are the inheritors of these glorious traditions and are fully alive to our responsibilities and obligations as framers of the future constitution of Pakistan.

In March, Jinnah, despite his declining health, made his only post-independence visit to East Pakistan. In a speech before a crowd estimated at 300,000, Jinnah stated (in English) that Urdu alone should be the national language, believing a single language was needed for a nation to remain united. The Bengali-speaking people of East Pakistan strongly opposed this policy, and in 1971 the official language issue was a factor in the region's secession to form the country of Bangladesh.