Mulla movie is about Mulla (Dileep) who happens to be the son of a silent sex worker but then grows as an orphan since she commits suicide and becomes the key henchman for Thampi Annan, a local don. All this is happening on the backdrop of Karakudu colony which happens to be the hub of all dark activities ranging from prostitution to harboring thieves, thugs and child trafficking.
The story takes a turn when Mulla chances upon a deserted child while on his assignment and with no other choice he gives it to Lalchi (Meera Nandan) whom he spots to be a regular in the train. Lalchi happens to be working in a bakery and is not left out as she has her own world of problems and in no time she comes back with the child and gives it back to Mulla.
He and his men try to bring up the child and Lalchi keeps visiting the child from time to time. These regular meetings lead to both of them falling in love and just when Mulla is looking at coming to terms with a new life , fate has something else in store for him.