"Shahid" was a biopic on slain human rights lawyer Shahid Azmi and his last project "CityLights", though not based on a real-life story, was about a migrant labourer.
"They all are thematically connected and deal with marginalisation, discrimination and a sense of justice," he told PTI in an interview.
"I am trying to chronicle the times that we live in. Years later, we will hear about our leaders and their achievements in a particular era or decade. But we won't hear stories of common man. I find these stories fascinating and feel there is a need to chronicle them."
The movie is based on the life of Aligarh University professor, Shrinivas Ramchandra Siras, who was suspended after he was filmed having sex with a rickshaw-puller in a sting operation.
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He fought and won against his suspension but was found dead under mysterious circumstances in 2010.
"Despite winning the court case, he was condemned to a life of loneliness by the society. He paid the price for going public. Desire does not know any gender... You can desire somebody from the opposite sex or somebody from the same sex and that's somebody's absolute personal choice."
Mehta was looking for an older actor to play Siras but finally decided to cast Bajpayee.
"It is Manoj's best performance. We always wanted to work together. For 'Aligarh' I was looking for a younger actor when our casting director Mukesh Chhabra suggested Manoj's name. There was no hesitation on Manoj's part because we share a level of trust."
Mehta seems to be drawn to real-life stories as his next, starring Kangana Ranaut, is again a biopic, which he will begin shooting in March, 2016.