This link gives the definition of Two-nation theory:
The two-nation theory is the basis of the creation of Pakistan. It states that Muslims and Hindus are two separate nations from every definition; therefore Muslims should have a separate homeland in the Muslim majority areas of India, where they can spend their lives according to the glorious teachings of Islam.
This link says that Muhammad Ali Jinnah was the first individual to come up with "Two Nation Theory".
But, some are saying that Veer Savarkar proposed it.
Veer Savarkar proposed two-nation theory, Jinnah implemented it: Bhupesh Baghel
Savarkar Laid Foundation of Two-Nation Theory, Congress Tells Amit Shah After Partition Swipe
Who was the first to conceive the "Two Nation Theory"?