The film opens with a frisky computer engineer struggling to set up his own software firm, Karthik, (model, TV star-turned hero, Madhavan) riding on a bike with a Walkman. Already married for two years to his doctor wife, Shakthi (Shalini), he arrives at a suburban railway station to pick her up for the day. Ashe waits for her anxiously while train after train departs.

Alaipayuthey oscillates between flashbacks and flash forwards to develop the narrative flow. It goes back to the time when they first met at a marriage, their meeting again and falling in love while travelling in local trains; deciding to have a court marriage and the ensuing predicaments they have to face from their families when the news reaches their ears. They are thrown out of home and come to stay together in an unfinished flat on a makeshift basis, with the kind courtesy of Karthik's colleagues. Meanwhile, they cut off all contact with their parents; it is only when Shakthi coincidentally chances upon her mother and elder sister Poorni in a local train that she discovers her father is hospitalized and his chances of living are very bleak. She is not allowed to visit her dad by Karthik, who tells her that they have no parents, and eventually her father expires. Nevertheless, Karthik plays Cupid to Poorni and this gives rise to a crisis in their marriage, which is threatening to fall apart due to miscommunication. In the denouement sequence, Karthik gets a million dollar US order and Shakthi comes out of her misunderstandings but gets struck by a car in the crossroads, landing up in the ICU of the same hospital…