Division of India, a consequence of Muslim League's two nation theory was based on the assumption that Hindus and Muslims are two different people and they can't live together. Jinnah and other Muslim leaders were worried that in an independent India caste Hindus will be dominant and rule.

At the time of Independence, Indian states were divided into multiple Administrative Zones or Provinces under direct British control. Also there were a lot of princely states ruled by native rulers. It was decided that all the provinces with Muslim majority will become part of Pakistan and rest will be part of India. Princely states were given an option to chose either India, Pakistan or remain independent. Now, Punjab and Bengal were huge states with no community being a dominant majority unlike all other states. So it was decided that these two states will also be divided. Eastern part of Punjab as well as West Bengal became Indian territory. As the states were being divided around the time of Indepnedence, there were huge riots in both the countries. Non Muslims from Pakistani punjab migrated to India while Muslims from Indian punjab migrated to Pakistan.

Since Pakistan was created for Muslims, everyone else migrated. On the other hand India was left for everyone who was not welcome in Pakistan, who didn't want to go to Pakistan or who couldn't go to Pakistan. India declared itself a secular and all inclusive country while Pakistan declared itself an Islamic country, though Jinnah wanted to just be a Muslim majority country and not a country ruled by Sharia.