Quaid-i-Azam had been ailing since long before Independence. By the time of Independence, he was quite an old man but still possessing a strong spirit. He hid the debilitating weakness caused by severely advanced tuberculosis. Researchers like Professor Stanley Wolpert believed that by the end, cancer had developed as well. Quaid-i-Azam was convinced that if word of illness leaked out, his opponents would make the most of it. He denied his illness even to himself and remained intent and unflinching so as to achieve the dream of millions of Muslims. He worked almost 24 hours a day and always preferred performing his national obligations to his own ailment.
At the time of independence, he was worn out by his intense struggle and opted to take the position of Governor General instead of that of Prime Minister. It had been proposed that the last Viceroy of India, Lord Mountbatten, be allowed to continue as a joint Governor General of both Pakistan and India. Quaid-i-Azam refused to accept this proposal as he felt that a joint Governor General would not be able to do justice to both the countries. He firmly believed that since Pakistan was a sovereign state, it must be sovereign in all respects with its own executive and government.
By this time, both aging and illness had mounted a terrible toll upon the Quaid. Although the flame still burnt bright, it was now at the cost of his own life. His physicians regularly advised him to take care of his health and to ease back on his work. But he never cared for it and kept on working hard day and night.
After the establishment of Pakistan, India created numerous problems. The refugee problem, the withholding of Pakistani assets by India, and the Kashmir problem were a real test for the Quaid. 
However, his indomitable will prevailed. He also worked out a sound economic policy, established an independent currency and the State Bank of Pakistan. He selected Karachi as the federal capital. His health deteriorated to such an extent, that he had to go to Ziarat for the restoration of his health. Despite the warning from his physicians, he went to Karachi to inaugurate the State Bank of Pakistan. This was his last public appearance.
