Mohammad Ali Jinnah (Urdu: محمد علی جناح ; December 25, 1876 – September 11, 1948) was a 20th century lawyer, politician, statesman and the founder of Pakistan. He is popularly and officially known in Pakistan as Quaid-e-Azam ("Great Leader") and Baba-e-Qaum ("Father of the Nation").

Jinnah served as leader of the All-India Muslim League from 1913 till Pakistan's independence on August 14, 1947 and Pakistan's first Governor-General from August 15, 1947 till his death on September 11, 1948. Jinnah rose to prominence in the Indian National Congress initially expounding ideas of Hindu-Muslim unity and helping shape the 1916 Lucknow Pact between the Muslim League and the Indian National Congress; he also became a key leader in the All India Home Rule League. He proposed a fourteen point constitutional reform plan to safeguard the political rights of Muslims in a self-governing India. Jinnah later advocated the Two-Nation Theory embracing the goal of creating a separate Muslim state as per the Lahore Resolution. The League won most reserved Muslim seats in the elections of 1946. After the British and Congress backed out of the Cabinet Mission Plan Jinnah called for a Direct Action Day to achieve the formation of Pakistan. The direct action by the Muslim League and its Volunteer Corps, resulted in massive rioting in Calcutta between Muslims and Hindus/Sikhs. As the Indian National Congress and Muslim League failed to reach a power sharing formula for a united India, it prompted both the parties and the British to agree to independence of Pakistan and India. As the first Governor-General of Pakistan, Jinnah led efforts to lay the foundations of the new state of Pakistan, frame national policies and rehabilitate millions of Muslim refugees who had migrated from India. He died in September 1948, just over a year after Pakistan gained independence from British India.

Jinnah was born Mahomedali Jinnahbhai in, some believe, Wazir Mansion, Karachi District, of lower Sindh. This is disputed as old textbooks mention Jhirk as his place of birth. Sindh had earlier been conquered by the British and was subsequently grouped with other conquered territories for administrative reasons to form the Bombay Presidency of British India. Although his earliest school records state that he was born on October 20, 1875, Sarojini Naidu, the author of Jinnah's first biography, gives the date as ”December 25, 1876”. Jinnah was the eldest of seven children born to Mithibai and Jinnahbhai Poonja. His father, Jinnahbhai (1857 – 1901), was a prosperous Gujarati merchant who had moved to Sindh from Kathiawar, Gujarat, before Jinnah's birth. His grandfather was Poonja Gokuldas Meghji, a Hindu Bhatia Rajput from Paneli village in Gondal state in Kathiawar. Jinnah's ancestors were Hindu Rajput who converted to Islam. Jinnah's family belonged to the Ismaili Khoja branch of Shi'a Islam, though Jinnah later converted to Twelver Khoja Shia Islam. The first-born Jinnah was soon joined by six siblings, brothers Ahmad Ali, Bunde Ali, and Rahmat Ali, and sisters Maryam, Fatima and Shireen. Their mother tongue was Gujarati; in time they also came to speak Kutchi, Sindhi and English. The proper Muslim names of Mr. Jinnah and his siblings, unlike those of his father and grandfather, are the consequence of the family's immigration to the Muslim state of Sindh. Jinnah was a restless student, he studied at several schools: at the Sindh-Madrasa-tul-Islam in Karachi; briefly at the Gokal Das Tej Primary School in Bombay; and finally at the Christian Missionary Society High School in Karachi, where, at age sixteen, he passed the matriculation examination of the University of Bombay.

In 1892, Jinnah was offered an apprenticeship at the London office of Graham's Shipping and Trading Company, a business that had extensive dealings with Jinnahbhai Poonja's firm in Karachi. Before he left for England, at his mother's urging, he married his distant cousin – Emibai Jinnah - who was two years his junior; she died a few months later. During his sojourn in England, his mother too would pass away. In London, Jinnah soon left the apprenticeship to study law instead, by joining Lincoln's Inn. It is said that the sole reason of Jinnah's joining Lincoln's Inn is that the welcome board of the Lincoln's Inn had the names of the world's all-time top-ten magistrates, and that this list was led by the name of Muhammad. No such board exists, although there is a mural which includes a picture of Muhammad. In three years, at age 19, he became the youngest Indian to be called to the bar in England. During his student years in England, Jinnah came under the spell of 19th-century British liberalism, like many other future Indian independence leaders. This education included exposure to the idea of the democratic nation and progressive politics. He admired William Gladstone and John Morley, British Liberal statesmen. An admirer of the Indian political leaders Dadabhai Naoroji and Sir Pherozeshah Mehta, he worked with other Indian students on the former's successful campaign to become the first Indian to hold a seat in the British Parliament.

By now, Jinnah had developed largely constitutionalist views on Indian self-government, and he condemned both the arrogance of British officials in India and the discrimination practiced by them against Indians. This idea of a nation legitimized by democratic principles and cultural commonalities was antithetical to the genuine diversity that had generally characterized the subcontinent. As an Indian intellectual and political authority, Jinnah would find his commitment to the Western ideal of the nation-state - developed during his English education – and the reality of heterogeneous Indian society to be difficult to reconcile during his later political career. The Western world not only inspired Jinnah in his political life. England had greatly influenced his personal preferences, particularly when it came to dress. Jinnah donned Western style clothing and he pursued the fashion with fervor. It is said he owned over 200 hand-tailored suits which he wore with heavily starched shirts with detachable collars. It is also alleged that he never wore the same silk tie twice. M C Chagla, a former colleague of Jinnah's, has stated that Jinnah was fond of eating pork, an act which is forbidden is Islam. The historian Stanley Wolpert has also alleged this in a book about Jinnah. The Pakistani government has banned books (including Wolpert's) which have mentioned this alleged dietary preference of Jinnah's.

During the final period of his stay in England, Jinnah came under considerable pressure to return home when his father's business was ruined. In 1896 he returned to India and settled in Bombay. Jinnah built a house in Malabar Hill, later known as Jinnah House. He became a successful lawyer, gaining particular fame for his skilled handling of the "Caucus Case". His reputation as a skilled lawyer prompted Indian leader Bal Gangadhar Tilak to hire him as defence counsel for his sedition trial in 1905. Jinnah argued that it was not sedition for an Indian to demand freedom and self-government in his own country, but Tilak received a rigorous term of imprisonment. When he returned to India his faith in liberalism and progressive politics was confirmed through his close association with three Indian National Congress stalwarts Gopal Krishna Gokhale, Pherozeshah Mehta and Surendranath Banerjee. These people had an influence in his early life in England and they would influence his later involvement in Indian politics.

In 1896, Jinnah joined the Indian National Congress, which was the largest Indian political organisation. Like most of the Congress at the time, Jinnah did not favour outright independence, considering British influences on education, law, culture and industry as beneficial to India. Jinnah became a member on the sixty-member Imperial Legislative Council. The council had no real power or authority, and included a large number of un-elected pro-Raj loyalists and Europeans. Nevertheless, Jinnah was instrumental in the passing of the Child Marriages Restraint Act, the legitimization of the Muslim waqf (religious endowments) and was appointed to the Sandhurst committee, which helped establish the Indian Military Academy at Dehra Dun. During World War I, Jinnah joined other Indian moderates in supporting the British war effort, hoping that Indians would be rewarded with political freedoms.

Jinnah had initially avoided joining the All India Muslim League, founded in 1906, regarding it as too Muslim oriented. However he decided to provide leadership to the Muslim minority. Eventually, he joined the league in 1913 and became the president at the 1916 session in Lucknow. Jinnah was the architect of the 1916 Lucknow Pact between the Congress and the League, bringing them together on most issues regarding self-government and presenting a united front to the British. Jinnah also played an important role in the founding of the All India Home Rule League in 1916. Along with political leaders Annie Besant and Tilak, Jinnah demanded "home rule" for India — the status of a self-governing dominion in the Empire similar to Canada, New Zealand and Australia. He headed the League's Bombay Presidency chapter.

In 1918, Jinnah married his second wife Rattanbai Petit ("Ruttie"), twenty-four years his junior. She was the fashionable young daughter of his personal friend Sir Dinshaw Petit, of an elite Parsi family of Mumbai. Unexpectedly there was great opposition to the marriage from Rattanbai's family and Parsi society, as well as orthodox Muslim leaders. Rattanbai defied her family and nominally converted to Islam, adopting (though never using) the name Maryam Jinnah, resulting in a permanent estrangement from her family and Parsi society. The couple resided in Mumbai, and frequently travelled across India and Europe. In 1919 she bore Jinnah his only child, daughter Dina Jinnah.

In 1924 Jinnah reorganized the Muslim League, of which he had been president since 1919, and devoted the next seven years attempting to bring about unity among the disparate ranks of Muslims and to develop a rational formula to effect a Hindu Muslim settlement, which he considered the precondition for Indian freedom. He attended several unity conferences, wrote the Delhi Muslim Proposals in 1927, pleaded for the incorporation of the basic Muslim demands in the Nehru report, and formulated the “Fourteen Points”

Jinnah broke with the Congress in 1920 when the Congress leader, Mohandas Gandhi, launched a law violating Non-Cooperation Movement against the British, which a temperamentally law abiding barrister Jinnah disapproved of. Unlike most Congress leaders, Gandhi did not wear western-style clothes, did his best to use an Indian language instead of English, and was deeply rooted to Indian culture. Gandhi's local style of leadership gained great popularity with the Indian people. Jinnah criticised Gandhi's support of the Khilafat Movement, which he saw as an endorsement of religious zealotry. By 1920, Jinnah resigned from the Congress, with a prophetic warning that Gandhi's method of mass struggle would lead to divisions between Hindus and Muslims and within the two communities. Becoming president of the Muslim League, Jinnah was drawn into a conflict between a pro-Congress faction and a pro-British faction.

In September 1923, Jinnah was elected as Muslim member for Bombay in the new Central Legislative Assembly. He showed great gifts as a parliamentarian, organized many Indian members to work with the Swaraj Party, and continued to press demands for full responsible government. He was so active on a wide range of subjects that in 1925 he was offered a knighthood by Lord Reading when he retired as Viceroy and Governor General. Jinnah replied: "I prefer to be plain Mr. Jinnah".

In 1927, Jinnah entered negotiations with Muslim and Hindu leaders on the issue of a future constitution, during the struggle against the all-British Simon Commission. The League wanted separate electorates while the Nehru Report favoured joint electorates. Jinnah personally opposed separate electorates, but then drafted compromises and put forth demands that he thought would satisfy both. These became known as the 14 points of Mr. Jinnah. However, they were rejected by the Congress and other political parties.

Jinnah's personal life and especially his marriage suffered during this period due to his political work. Although they worked to save their marriage by travelling together to Europe when he was appointed to the Sandhurst committee, the couple separated in 1927. Jinnah was deeply saddened when Rattanbai died in 1929, after a serious illness.

At the Round Table Conferences in London, Jinnah was disillusioned by the breakdown of talks. After the failure of the Round Table Conferences, Jinnah returned to London for a few years. In 1936, he returned to India to re-organize the Muslim League and contest the elections held under the provisions of the Act of 1935.

Jinnah would receive personal care and support as he became more ill during this time from his sister Fatima Jinnah. She lived and travelled with him, as well as becoming a close advisor. She helped raise his daughter, who was educated in England and India. Jinnah later became estranged from his daughter, Dina Jinnah, after she decided to marry Parsi-born Christian businessman, Neville Wadia (even though he had faced the same issues when he married Rattanbai in 1918). Jinnah continued to correspond cordially with his daughter, but their personal relationship was strained. Dina continued to live in India with her family.

Prominent Muslim leaders like the The Aga Khan, Choudhary Rahmat Ali and Sir Muhammad Iqbal made efforts to convince Jinnah to return from London (where he had moved to in 1931 and planned on permanently relocating in order to practice in the Privy Council Bar) to India and take charge of a now-reunited Muslim League. In 1934 Jinnah returned and began to re-organise the party, being closely assisted by Liaquat Ali Khan, who would act as his right-hand man. In the 1937 elections to the Central Legislative Assembly, the League emerged as a competent party, capturing a significant number of seats under the Muslim electorate, but lost in the Muslim-majority Punjab, Sindh and the North-West Frontier Province. Jinnah offered an alliance with the Congress – both bodies would face the British together, but the Congress had to share power, accept separate electorates and the League as the representative of India's Muslims. The latter two terms were unacceptable to the Congress, which had its own national Muslim leaders and membership and adhered to secularism. Even as Jinnah held talks with Congress president Rajendra Prasad, Congress leaders suspected that Jinnah would use his position as a lever for exaggerated demands and obstruct government, and demanded that the League merge with the Congress. The talks failed, and while Jinnah declared the resignation of all Congressmen from provincial and central offices in 1938 as a "Day of Deliverance" from Hindu domination, some historians assert that he remained hopeful for an agreement.

In a speech to the League in 1930, Sir Muhammad Iqbal mooted an independent state for Muslims in "northwest India." Choudhary Rahmat Ali published a pamphlet in 1933 advocating a state called "Pakistan". Following the failure to work with the Congress, Jinnah, who had embraced separate electorates and the exclusive right of the League to represent Muslims, was converted to the idea that Muslims needed a separate state to protect their rights. Jinnah came to believe that Muslims and Hindus were distinct nations, with unbridgeable differences — a view later known as the Two Nation Theory. Jinnah declared that a united India would lead to the marginalization of Muslims, and eventually civil war between Hindus and Muslims. This change of view may have occurred through his correspondence with Iqbal, who was close to Jinnah. In the session in Lahore in 1940, the Pakistan resolution was adopted as the main goal of the party. The resolution was rejected outright by the Congress, and criticised by many Muslim leaders like Maulana Abul Kalam Azad, Khan Abdul Ghaffar Khan, Syed Ab'ul Ala Maududi and the Jamaat-e-Islami. On July 26, 1943, Jinnah was stabbed and wounded by a member of the extremist Khaksars in an attempted assassination.

Muhammad Ali Jinnah founded Dawn in 1941, a major newspaper that helped him propagate the League's point of views. During the mission of British minister Stafford Cripps, Jinnah demanded parity between the number of Congress and League ministers, the League's exclusive right to appoint Muslims and a right for Muslim-majority provinces to secede, leading to the breakdown of talks. Jinnah supported the British effort in World War II, and opposed the Quit India movement. During this period, the League formed provincial governments and entered the central government. The League's influence increased in the Punjab after the death of Unionist leader Sikander Hyat Khan in 1942. Gandhi held talks fourteen times with Jinnah in Bombay in 1944, about a united front — while talks failed, Gandhi's overtures to Jinnah increased the latter's standing with Muslims.

In the 1946 elections for the Constituent Assembly of India, the Congress won most of the elected seats, while the League won a large majority of Muslim electorate seats. The 1946 British Cabinet Mission to India released a plan on May 16, calling for a united Indian state comprising considerably autonomous provinces, and called for "groups" of provinces formed on the basis of religion. A second plan released on June 16, called for the separation of India along religious lines, with princely states to choose between accession to the dominion of their choice or independence. The Congress, fearing India's fragmentation, criticised the May 16 proposal and rejected the June 16 plan. Jinnah gave the League's assent to both plans, knowing that power would go only to the party that had supported a plan. After much debate and against Gandhi's advice that both plans were divisive, the Congress accepted the May 16 plan while condemning the grouping principle. Jinnah decried this acceptance as "dishonesty", accused the British negotiators of "treachery", and withdrew the League's approval of both plans. The League boycotted the assembly, leaving the Congress in charge of the government but denying it legitimacy in the eyes of many Muslims.

Jinnah gave a precise definition of the term 'Pakistan' in 1941 at Lahore in which he stated:

Some confusion prevails in the minds of some individuals in regard to the use of the work 'Pakistan'. This word has become synonymous with the Lahore resolution owing to the fact that it is a convenient and compendious method of describing [it].... For this reason the British and Indian newspapers generally have adopted the word 'Pakistan' to describe the Moslem demand as embodied in the Lahore resolution.

Jinnah issued a call for all Muslims to launch "Direct Action" on August 16 to "achieve Pakistan". Strikes and protests were planned, but violence broke out all over India, especially in Calcutta and the district of Noakhali in Bengal, and more than 7,000 people were killed in Bihar. Although viceroy Lord Wavell asserted that there was "no satisfactory evidence to that effect", League politicians were blamed by the Congress and the media for orchestrating the violence. Interim Government portfolios were announced on October 25, 1946. Muslim Leaguers were sworn in on October 26, 1946. The League entered the interim government, but Jinnah refrained from accepting office for himself. This was credited as a major victory for Jinnah, as the League entered government having rejected both plans, and was allowed to appoint an equal number of ministers despite being the minority party. The coalition was unable to work, resulting in a rising feeling within the Congress that independence of Pakistan was the only way of avoiding political chaos and possible civil war. The Congress agreed to the division of Punjab and Bengal along religious lines in late 1946. The new viceroy Lord Mountbatten of Burma and Indian civil servant V.P. Menon proposed a plan that would create a Muslim dominion in West Punjab, East Bengal, Baluchistan and Sindh. After heated and emotional debate, the Congress approved the plan. The North-West Frontier Province voted to join Pakistan in a referendum in July 1947. Jinnah asserted in a speech in Lahore on October 30, 1947 that the League had accepted independence of Pakistan because "the consequences of any other alternative would have been too disastrous to imagine."

The independent state of Pakistan, created on August 14, 1947, represented the outcome of a campaign on the part of the Indian Muslim community for a Muslim homeland which had been triggered by the British decision to consider transferring power to the people of India. While giving an interview to American press representatives in July 1942, when asked by one of the journalists whether the Muslims were a nation or not, Jinnah replied:

We are a nation with our own distinctive culture and civilization, language and literature, art and architecture, names and nomenclature, sense of values and proportion, legal laws and moral codes, customs and calendar, history and traditions, aptitudes and ambitions, in short, we have our own distinctive outlook on life and of life. By all cannons of international law we are a nation.

A controversy has raged in Pakistan about whether Jinnah wanted Pakistan to be a secular state or an Islamic state. His views as expressed in his policy speech on August 11, 1947 said:

There is no other solution. Now what shall we do? Now, if we want to make this great State of Pakistan happy and prosperous, we should wholly and solely concentrate on the well-being of the people, and especially of the masses and the poor. If you will work in co-operation, forgetting the past, burying the hatchet, you are bound to succeed. If you change your past and work together in a spirit that everyone of you, no matter to what community he belongs, no matter what relations he had with you in the past, no matter what is his colour, caste or creed, is first, second and last a citizen of this State with equal rights, privileges, and obligations, there will be no end to the progress you will make. I cannot emphasize it too much. We should begin to work in that spirit and in course of time all these angularities of the majority and minority communities, the Hindu community and the Muslim community, because even as regards Muslims you have Pathans, Punjabis, Shias, Sunnis and so on, and among the Hindus you have Brahmins, Vashnavas, Khatris, also Bengalis, Madrasis and so on, will vanish. Indeed if you ask me, this has been the biggest hindrance in the way of India to attain the freedom and independence and but for this we would have been free people long long ago. No power can hold another nation, and specially a nation of 400 million souls in subjection; nobody could have conquered you, and even if it had happened, nobody could have continued its hold on you for any length of time, but for this. Therefore, we must learn a lesson from this. You are free; you are free to go to your temples, you are free to go to your mosques or to any other place or worship in this State of Pakistan. You may belong to any religion or caste or creed that has nothing to do with the business of the State. As you know, history shows that in England, conditions, some time ago, were much worse than those prevailing in India today. The Roman Catholics and the Protestants persecuted each other. Even now there are some States in existence where there are discriminations made and bars imposed against a particular class. Thank God, we are not starting in those days. We are starting in the days where there is no discrimination, no distinction between one community and another, no discrimination between one caste or creed and another. We are starting with this fundamental principle that we are all citizens and equal citizens of one State. The people of England in course of time had to face the realities of the situation and had to discharge the responsibilities and burdens placed upon them by the government of their country and they went through that fire step by step. Today, you might say with justice that Roman Catholics and Protestants do not exist; what exists now is that every man is a citizen, an equal citizen of Great Britain and they are all members of the Nation. Now I think we should keep that in front of us as our ideal and you will find that in course of time Hindus would cease to be Hindus and Muslims would cease to be Muslims, not in the religious sense, because that is the personal faith of each individual, but in the political sense as citizens of the State. Jinnah, August 11, 1947 – presiding over the constituent assembly.

While this may seem to be an indication that Jinnah wanted a secular state, he also referred to Islam and Islamic principles:

The constitution of Pakistan has yet to be framed by the Pakistan Constituent Assembly. I do not know what the ultimate shape of this constitution is going to be, but I am sure that it will be of a democratic type, embodying the essential principle of Islam. Today, they are as applicable in actual life as they were 1,300 years ago. Islam and its idealism have taught us democracy. It has taught equality of man, justice and fairplay 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 any case Pakistan is not going to be a theocratic State to be ruled by priests with a divine mission. We have many non-Muslims -- Hindus, Christians, and Parsis -- but they are all Pakistanis. They will enjoy the same rights and privileges as any other citizens and will play their rightful part in the affairs of Pakistan.Broadcast talk to the people of the United States of America on Pakistan recorded February, 1948.

It has been argued by many people that in this speech Jinnah wanted to point out that Pakistan would be a secular state as mostly people think that an Islamic state is a theocratic state. This perception, however, is wrong and is misinterpreted; the reason is that a true Islamic state is not a theocratic state, as stated by Jinnah in his speech.

On the opening ceremony of the state bank of Pakistan Jinnah pointed out that the financial setup of the state should be based on Islamic economic system.

We must work our destiny in our own way and present to the world an economic system based on true Islamic concept of equality of manhood and social justice. We will thereby be fulfilling our mission as Muslims and giving to humanity the message of peace which alone can save it and secure the welfare, happiness and prosperity of mankind. Speech at the opening ceremony of State Bank of Pakistan, Karachi July 1, 1948

It appears that Jinnah felt the state of Pakistan should stand upon Islamic tradition in culture, civilization and national identity rather than on the principles of Islam as a theocratic state. In 1937, Jinnah further defended his ideology of equality in his speech to the All-India Muslim League in Lucknow where he stated, "Settlement can only be achieved between equals." He also had a rebuttal to Nehru's statement which argued that the only two parties that mattered in India were the British Raj and INC. Jinnah stated that the Muslim League was the third and "equal partner" within Indian politics.

Along with Liaquat Ali Khan and Abdur Rab Nishtar, Muhammad Ali Jinnah represented the League in the Division Council to appropriately divide public assets between India and Pakistan. The assembly members from the provinces that would comprise Pakistan formed the new state's constituent assembly, and the Military of British India was divided between Muslim and non-Muslim units and officers. Indian leaders were angered at Jinnah's courting the princes of Jodhpur, Bhopal and Indore to accede to Pakistan – these princely states were not geographically aligned with Pakistan, and each had a Hindu-majority population.

Jinnah became the first Governor-General of Pakistan and president of its constituent assembly. Inaugurating the assembly on August 11, 1947, Jinnah spoke of an inclusive and pluralist democracy promising equal rights for all citizens regardless of religion, caste or creed. This address is a cause of much debate in Pakistan as, on its basis, many claim that Jinnah wanted a secular state while supporters of Islamic Pakistan assert that this speech is being taken out of context when compared to other speeches by him. On October 11, 1947, in an address to Civil, Naval, Military and Air Force Officers of Pakistan Government, Karachi, he said:

We should have a State in which we could live and breathe as free men and which we could develop according to our own lights and culture and where principles of Islamic social justice could find free play.

On February 21, 1948, in an address to the officers and men of the 5th Heavy Ack Ack and 6th Light Ack Ack Regiments in Malir, Karachi, he said:

You have to stand guard over the development and maintenance of Islamic democracy, Islamic social justice and the equality of manhood in your own native soil. With faith, discipline and selfless devotion to duty, there is nothing worthwhile that you cannot achieve.

The office of Governor-General was ceremonial, but Jinnah also assumed the lead of government. The first months of Pakistan's independence were absorbed in ending the intense violence that had arisen in the wake of acrimony between Hindus and Muslims. Jinnah agreed with Indian leaders to organise a swift and secure exchange of populations in the Punjab and Bengal. He visited the border regions with Indian leaders to calm people and encourage peace, and organised large-scale refugee camps. Despite these efforts, estimates on the death toll vary from around two hundred thousand, to over a million people. The estimated number of refugees in both countries exceeds 15 million. The then capital city of Karachi saw an explosive increase in its population owing to the large encampments of refugees, which personally affected and depressed Jinnah.

In his first visit to East Pakistan, under the advice of local party leaders, Jinnah stressed that Urdu alone should be the national language; a policy that was strongly opposed by the Bengali people of East Pakistan (now Bangladesh). This opposition grew after he controversially described Bengali as the language of Hindus.

Jinnah authorised force to achieve the annexation of the princely state of Kalat and suppress the insurgency in Baluchistan. He controversially accepted the accession of Junagadh — a Hindu-majority state with a Muslim ruler located in the Saurashtra peninsula, some 400 kilometres (250 mi) southeast of Pakistan — but this was annulled by Indian intervention. It is unclear if Jinnah planned or knew of the tribal invasion from Pakistan into the kingdom of Jammu and Kashmir in October 1947, but he did send his private secretary Khurshid Ahmed to observe developments in Kashmir. When informed of Kashmir's accession to India, Jinnah deemed the accession illegitimate and ordered the Pakistani army to enter Kashmir. However, Gen. Auchinleck, the supreme commander of all British officers informed Jinnah that while India had the right to send troops to Kashmir, which had acceded to it, Pakistan did not. If Jinnah persisted, Auchinleck would remove all British officers from both sides. As Pakistan had a greater proportion of Britons holding senior command, Jinnah cancelled his order, but protested to the United Nations to intercede.

Through the 1940s, Jinnah suffered from tuberculosis; only his sister and a few others close to him were aware of his condition. In 1948, Jinnah's health began to falter, hindered further by the heavy workload that had fallen upon him following Pakistan's independence from British Rule. Attempting to recuperate, he spent many months at his official retreat in Ziarat. According to his sister, he suffered a hemorrhage on September 1, 1948; doctors said the altitude was not good for him and that he should be taken to Karachi. Jinnah was flown back to Karachi from Quetta. Jinnah died at 10:20 p.m. at the Governor-General's House in Karachi on September 11, 1948, just over a year after Pakistan's independence.

It is said that when the then Viceroy of India, Lord Louis Mountbatten, learned of Jinnah's ailment he said 'had they known that Jinnah was about to die, they'd have postponed India's independence by a few months as he was being inflexible on Pakistan'.

Jinnah was buried in Karachi. His funeral was followed by the construction of a massive mausoleum, Mazar-e-Quaid, in Karachi to honour him; official and military ceremonies are hosted there on special occasions. He had two separate Funeral prayers one was held privately at Mohatta Palace in a room of the Governor-General's House at which Yusuf Haroon, Hashim Raza and Aftab Hatim Alvi were present at the Namaz-e-Janaza held according to Shia rituals and was led by Syed Anisul Husnain, while Liaquat Ali Khan waited outside. After the Shia ritual, the major public Funeral prayers were led by Allamah Shabbir Ahmad Usmani a renowned mainstream Muslim (Sunni) scholar and attended by masses from all over Pakistan. This funeral was well on record and supported by pictures as well.

Dina Wadia remained in India after independence, before ultimately settling in New York City. Jinnah's grandson, Nusli Wadia, is a prominent industrialist residing in Mumbai. In the 1963 – 1964 elections, Jinnah's sister Fatima Jinnah, known as Madar-e-Millat ("Mother of the Nation"), became the presidential candidate of a coalition of political parties that opposed the rule of President Ayub Khan, but lost the election.

The Jinnah House in Malabar Hill, Bombay, is in the possession of the Government of India but the issue of its ownership has been disputed by the Government of Pakistan. Jinnah had personally requested Indian Prime Minister Jawaharlal Nehru to preserve the house and that one day he could return to Mumbai. There are proposals for the house to be offered to the Government of Pakistan to establish a consulate in the city, as a goodwill gesture, but Dina Wadia has also laid claim to the property, claiming that Hindu Law is applicable to Jinnah as he was a Khoja Shia.

After Jinnah died, Fatima Jinnah had asked the court to execute Jinnah's will under Shia law. Jinnah's family belonged to the Ismaili Khoja branch of Shi'a Islam, but Jinnah left that branch in 1901. Vali Nasr says Jinnah "was an Ismaili by birth and a Twelver Shia by confession, though not a religiously observant man." In a 1970 legal challenge, Hussain Ali Ganji Walji claimed Jinnah had converted to Sunni Islam, but the court rejected this claim in 1976, effectively accepting the Jinnah family as Shia. Publicly, Jinnah had a non-sectarian stance and "was at pains to gather the Muslims of India under the banner of a general Muslim faith and not under a divisive sectarian identity." In 1970, a court decision stated that Jinnah's "secular Muslim faith made him neither Shia nor Sunni", and in 1984 the court maintained that "the Quaid was definitely not a Shia". Liaquat H. Merchant elaborates that "he was also not a Sunni, he was simply a Muslim".