Sethurama Iyer CBI is the Sequel of Malayalam movie Jagratha . SethuramaIyer (Mammootty) who is a sharp and highly intelligent investigative officer of the CBI and was on vacation in Kerala, where he happened to meet Alex (Kalabhavan Mani) who is a convicted serial killer and who was about to be hanged. Alex was convicted of six murders but Alex confesses to Iyer that he had killed only five people and the sixth man, a financier was killed by someone else and he got blamed for it.
Some how Iyer believes Alex and he decides to look into this case. Sethurama Iyer put his team together Chacko (Mukesh), Vikram (Jagathi) and Ganesh (Vineeth Kumar) and starts the investigation. Iyer's two nieces Rashmi and Rachana (Navya and Nandana) also gets involved in the case. Finally Iyer and his team isolate the actual murderer in the last case.