Mullavalliyum Thenmavum movie is about Shelly ( Kunchako Boban ) and Rajasree ( Chaya Singh ) who are students at fine arts college and they fall in love during college days. Their parents oppose for their marriage and they elope and end up with Dr. Alex ( Lalu Alex ). Rajasree asks Shelly to wait for the marriage, as she wants to do it with their parents permission.
Dr. Alex gets an assignment for Shelly, to make a house boat for the tourism department. But he cannot complete the making of the boat and another architect, Andre enters into their life.