Aayudham movie is a satirical enquiry based on the recent development in the state politics. The City Police Commissioner Mahendra Varma, in a bid to round off his duties, first arrests whomever he can lay hands on and then zeroes in on Anwar, the son of Abdullah Mukri. Anwar is arrested from Chennai on the basis of a call from his mobile, made to one of the terrorists, who drops the device at the blast site.
The state Chief Minister Madhavan (Thilakan) who is is convinced that the investigation is not proceeding in the right direction and decides to bring in the Crime Branch to conduct the probe. Acting on the advice of the Chief Secretary, he puts Hrishikesh IPS (Suresh Gopi) who is the Crime Branch DIG, in charge of the investigation.
After securing the assurance of the Chief Minister that there will not be any political interference, Hrishikesh ropes in the services of two Police Officers - Hamza and Rappai. As the investigation progresses, the plot behind the blast slowly unfolds.