Set against a backdrop of immense political turmoil is the country. Hazaaron Khwaishein Aisi is the story of Siddharth Tyabji (Kay Kay Menon), the son of leftist liberal parents, Geeta Rao (Chitrangda Singh) , the daughter of a brilliant but conservative scientist and Vikram Malhotra (Rohan Ahuja), a small-town boy totally cotemptuous of his father's inconsequential political idealism.

The story begins in a prestigious Delhi college where the three have completed their under graduation and are charting out their future. Geeta is in love with Siddharth but politics is Siddharth's first love. Vikram, however, is madly in love with Geeta.

Siddharth decided to join Naxal movement in the villages of Bihar to fight for the cause of the peasants there. Geeta goes to England for further studies. Vikram follows up with the connection he has 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 journalists 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 any 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 loved this man alive. So despite his feelings for Siddharth, Vikram decides to help him.

Through a strange twist of circumstances, Vikram ends up in the same hospital where Siddharth is being treated. Siddharth, with the help of his comrades, escapes. Vikram is picked up by the police and beaten up brutally.

Siddharth finally abandons his passion for politics and decides to study medicine in England. He asks Geeta to come with him. She refuses.

Geeta goes back to the village with Vikram and dedicates her life to taking care of Vikram who is now confined to a wheelchair and is only a shadow of that person he once used to be. At the end our protagonists fins themselves in situation that only a quirk of destiny could have decided for them.