Mamun Rashid was handed over to his family in presence of state government officials and Border Security Force personnel at the Gede checkpoint yesterday, from where he started for his village in Rajsahi district.
"Rashid has left for his home in Bangladesh yesterday," Nadia District Magistrate Sumit Gupta said.
The BSF had arrested Rashid, thinking him to be an infiltrator, after he crossed the Shutia border on November 2, 2015.
He had no documents of identity and was talking disjointedly, officials said.
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The district administration then referred him to an NGO - Nakashipara Nirmal Hriday Samity, run by Moslem Munshi, who has been treating such patients for a number of years.
"I treated and nursed him, as I have been doing for others. Everyday, I bathed him, shaved him, gave him some physical exercise. He became fit within four months, and told me his name and address," Munshi said.
Munshi said he sent a letter to Rashid's father Abdul Karim in Bangladesh, and his maternal uncle Nurul came to India and met him in February, 2016.
Following this, the repatriation process started but it took longer than usual because of an error in Rashid's documents, the officials said.
"I searched for my son Mamun for the last three years. I had taken him to many physicians in Bangladesh to cure his mental condition. I am very happy to get back my son. I bow down my head to Moslem Munshi for him and arranging his return," Abdul Karim said in a choked voice.
An elated Rashid added, "I am happy to return home at last. I am grateful to Moslem mama. I have a desire to come here again with passport and visa to meet him.