The Indian National Congress agreed in 1947 to the partition of the country mainly because

The Indian National Congress was fundamentally opposed to the partition of India and never fully accepted the Two Nation Theory. However, by 1947, the country was witnessing extreme communal violence and bloodbath following the Direct Action Day and subsequent riots in regions like Noakhali and Punjab.

The Congress leadership, including Sardar Patel and Jawaharlal Nehru, realized that the interim government was unable to function effectively due to the deadlock with the Muslim League. They concluded that accepting partition was a necessary evil to prevent further large scale communal massacres and to ensure a strong, centralized administration for the rest of India. They believed that a peaceful, partitioned India was better than a united India engulfed in a perpetual civil war. Therefore, avoiding large scale communal riots was the primary reason for their agreement.