‘Aligarh’ is a biographical drama and happens to be insured by a real-life incident about a professor who was suspended from his job because of his sexual orientation. Set in a city of Uttar Pradesh and based on true events, the plot revolves around Dr Shrinivas Ramchandra Siras who taught Marathi at Aligarh Muslim University.
The film starts off on the premises of Aligarh University, the very 'Urdu dominated' place where Prof. Shrinivas Siras (Manoj Bajpayee) happens to teach Marathi to the students. The film gradually moves onto capturing the 'intimate moments' between Prof. Shrinivas Siras and a rickshaw driver Irfan. The moment they get intimate with each other, two 'reporters' (who claim to be from TV 100 channel) do a sting operation on the duo. As Siras and Irfan get caught in the act, Dr Zuber Khan, Dr Firoz Majid, Dr Shadab Qureshi and Prof. A. K. Murtuza from the university enters the room. Even though Dr Shadab Qureshi (who also happens to be the college's PRO) assures Siras that he will not leak his intimate video, he goes back on his words and tells the media all about the incident.
The next day morning sees all the newspapers and channels screaming about Siras' incident, which also results in a mob burning his effigies, human protests etc. All of this results in Prof. Siras being suspended from the college and gets told to vacant the quarters within a week's time. Meanwhile, a young and 'fire in the belly' journalist Deepu Sebastian (Rajkummar Rao) starts writing about the case arming himself with a thorough investigation, because he feels that Siras is not guilty and could have been framed. Initially, Siras is reluctant to speak to Deepu about the incident because the latter is a journalist.
After a few meetings, Siras develops full faith in Deepu and he confides the whole incident that had taken place that night. While on one hand, Deepu goes all out to get justice for Siras, on the other hand, the court case against Siras only gets prolonged day after day. After days and days of struggle, when Deepu finally succeeds in being the 'agent of change' for Siras to get justice, a drunk Siras tells Deepu on the phone that he strongly feels that he should get settled in the US as that's where people of his sexual orientation get accepted with open arms.