Set against a backdrop of immense political turmoil in the country, Hazaaron Khwaishein Aisi is the story of Siddharth Tyabji, Geeta Rao and Vikram Malhotra. Geeta is in love with Siddharth but politics is Siddharth's first love. Vikram, however, is madly in love with Geeta.

Siddharth decides to join the Naxal movement in the villages of Bihar while Geeta goes to England for further studies. Vikram follows up with the connections he's made over the years in college to become a 'fixer' in the corridors of power in a country that is in the throes of political chaos.

Five years pass by. Vikram, now the toast of the town, accidentally meets Geeta at a party. She is now a journalist but suffers an unhappy marriage. Hoping to move in when the time is right, Vikram follows Geeta on one of her journalistic trips into a village. Only there he discovers that Geeta is still carrying on her affair with Siddharth.

Geeta eventually joins Siddharth's movement in Bihar and soon they get married. It's 1975. A state of Internal Emergency is declared in the country. For Vikram, things couldn't be better. He is on the right side of the power equation but Geeta and Siddharth are in trouble.

Still madly in love with her, Vikram uses his connections to save Geeta and get her back to Delhi. At the same time, he gets word that the police have orders to kill Siddharth. He could very well leave Siddharth there to die. But he knows it is important to the only woman he'd ever loved.

Through a strange twist of circumstances, Vikram is picked up by the police and beaten up so brutally that he becomes a vegetable.

Siddharth finally abandons his passion for politics and decides to study medicine in England. He asks Geeta to come with him. Does Geeta agree to go with Siddharth or does she dedicate her life to taking care of Vikram?

At the end our protagonists find themselves in situations that only the quirk of destiny could decide.