The guide takes Jinnah to 1947 where, at the Cromwell Conference with Lord Mountbatten, Jinnah demanded a homeland for Indian Muslims. After World War II, the British Imperial Government intends to withdraw and grant independence to the subcontinent. This would mean a Hindu-dominated state. Religious tensions between Hindus and Muslims were increasing after the Second World War. Flashbacks resume when the Guide recounts the marital life of Jinnah, when he fell in love and married a Parsi named Rattanbai Petit, later known against the will of her parents, mainly on grounds of religion and the difference in their ages. In 1922, Jinnah faces political isolation as he devoted every spare moment to be the voice of moderation in a nation torn by Hindu-Muslim antipathy. That created tension between Rattanbai and Jinnah. She finally leaves him with their daughter in September 1922, and they eventually separate in 1927. Rattanbai died of cancer on 18 February 1929. The death of Rattanbai had a huge impact on Jinnah's life and his fight for Pakistan. He went back to British India in order to start a political journey of the two-nation theory. In 1940, the Muslim League annual conference is held from 22 to 24 March. Jinnah addresses thousands of Muslims and gives them the assurance of the birth of Pakistan.
The Guide questions Jinnah as to who he loves the most apart from Ruttie and Fatima. He then mentioned his daughter, who married a Parsi boy without his permission.
While he was addressing a Muslim League conference in 1947, Muslims fanatics attacked the conference and argued that if Pakistan is to be a Muslim state, it cannot give equal rights to women and non-Muslims. Jinnah replies that Islam doesn't need fanatics but people with vision who can build the country. However, the partition of India was carried out, and the Guide and Jinnah saw the massacre of Muslims in migration done by Hindus and Sikhs. Jinnah is sworn in as the first Governor-General of Pakistan and announces Liaqat Ali Khan as the first Prime Minister of Pakistan.
After independence and the end of British rule, Pakistan stands as a new nation and sanctuary for the Muslims of the subcontinent. Jinnah is given the title of Quaid-e-Azam of Pakistan. Jinnah waits for the first train carrying Muslims who left India for Pakistan, but when the train arrives, they are all found dead save for one infant child. Fatimah and Lady Edwina Mountbatten visit refugees and Lady Mountbatten learns the importance of independence. Mountbatten betrays Jinnah as the Hindu Maharaja of Kashmir, Sir Hari Singh, stalls his decision on which nation to join. With the population in revolt in October 1947, aided by Pakistani irregulars, the Maharaja accedes to India; Indian troops are airlifted in. Jinnah objects to that and orders that Pakistani troops move into Kashmir, which leads to a war between India and Pakistan then and afterward from time to time in the Kashmir conflict.
The film jumps into a final fictional scene of Lord Louis Mountbatten, 1st Earl Mountbatten of Burma (last Viceroy of India) in a Heavenly Court. Jinnah is fighting a case against him over his betrayal. The film ends with Jinnah and his angel judge traveling back in time to the scene of Muslim refugees. Jinnah expresses his sorrow over the plight of the refugees during the division of Punjab. They chant "Pakistan Zindabad" in response, which ends the film.