Two nation theory means a separate nation for Muslims and Allama Iqbal wanted a separate nation for Mulsims. I gave numerous quotes from him.
"I would like to see the Punjab, North-West Frontier Province, Sind and Baluchistan amalgamated into a single state. Self-government within the British Empire, or without the British Empire, the formation of a consolidated Northwest Indian Muslim state appears to me to be the final destiny of the Muslims, at least of Northwest India." - 1930
"A separate federation of Muslim Provinces, reformed on the lines I have suggested above, is the only course by which we can secure a peaceful India and save Muslims from the domination of Non-Muslims. Why should not the Muslims of North-West India and Bengal be considered as nations entitled to self-determination just as other nations in India and outside India are." - 1937
"There is only one way out. Muslims should strengthen Jinnah's hands. They should join the Muslim League. Indian question, as is now being solved, can be countered by our united front against both the Hindus and the English. Without it, our demands are not going to be accepted. People say our demands smack of communalism. This is sheer propaganda. These demands relate to the defence of our national existence.... The united front can be formed under the leadership of the Muslim League. And the Muslim League can succeed only on account of Jinnah. Now none but Jinnah is capable of leading the Muslims."
Muhammad Iqbal - Wikipedia, the free encyclopedia
Sarvarkar wanted all the Muslims of British India, including what is now Pakistan, to leave the subcontinent and form a country somewhere in the Middle East..that is not what we had in mind.
Two-Nation Theory - Wikipedia, the free encyclopedia
Settle Kashmir dispute and Sir Creek dispute and then maybe we can think about being allies.