Anjali Menon, a reporter working with Mathrubhumi, receives a letter from a man identifying himself as 'Arjunan', saying he was the sole witness to the murder of former District Collector Firose Mooppan.

After receiving anonymous calls threatening her and her family's safety, Anjali schedules a meeting with Arjunan, with the assistance of Circle Inspector Sebastian.

While waiting for Arjunan, a young man named Roy Mathew, sits with Anjali due to a scarcity of free tables, has a coffee and leaves.

Realizing that Anjali's phone is being tapped, Roy stages a drama that allows him to follow the trackers, leading him to Aby Abraham, the Managing Director of City Mall.

With the help of Thankappan a peon at the Collector's Office, Roy and Anjali attain the blueprints of the abandoned Kochi Metro Rail project, which was shut down following Firose's death.

Roy realizes that Aby Abraham, along with his friends Salim Memmen, Rajan Thomas and Unni Natarajan, would have to give up their properties lying on government land, if the project had gone through, and suspects that they had colluded to murder Firose.

Realizing Aby and his partners' double-cross, Roy calls for a press meet, and publicly admits that he is the eponymous Arjunan, saying he has all important evidences against the perpetrators, and that he wishes to submit them to the law.

Roy appears in front of the panel, submitting the documents and the recording, admitting that he is not the real Arjunan, but a common civilian who was pulled into the controversy by the media.

"[4] In Arjunan Saakshi, the lead character Roy Mathew is played by Prithviraj, who started working on the film much before the completion of Santosh Sivan's Urumi and Lijo Jose Pellissery's City of God.

[7] Ann Augustine, who debuted through Lal Jose's Elsamma Enna Aankutty in 2010, plays the role of an investigative journalist and a city-bred youngster Anjali Menon, who happens to get involved in certain social issues.