The film opens on a rainy night. A woman trying to hire an auto standing by the kerb, notices an unconscious girl in the back seat. She proceeds to call the police realizing something is amiss, but is chased by a man seated in the driver's seat.
The scene then shifts to a New Year celebration by the beach where a cardboard box atop a car attracts the attention of revellers. The police are called. A similar box is also found in a park. Amputated male arms are found in the boxes and the case is put onto J. Krishnan, known as J.K. (Cheran), of the CB-CID. He is a brooding ex-cop who shifted from law and enforcement, paying the price for honesty, and at present is searching for his sister Charu who disappeared six months prior. Prakash (Shankar) and Tamilselvi (Dipa Shah) are two juniors who are put onto the case to assist JK.
At the morgue, they meet Judas Iscariot (Jayaprakash), a medical examiner, to investigate the hands. Judas, mildly esoteric, often draws parallels between JK and Jiddu Krishnamurthi. JK is able to identify one pair of hands as belonging to auto-driver Moorthy and follows the lead. Through a local goon Surendra, they single out a middleman Rajamanickam.
JK gets a cop to give him sensitive information stored in files at the ACP's office while still trying to trace his sister. He often goes and visits the place where his sister was last seen in the hope of getting clues. Meanwhile, Rajamanickam is tortured and his hands are amputated and displayed as well. A plain clothes constable gives a tip that Rajamanickam's bike is at a lodge in Triplicane. JK goes to investigate but finds a man, Raghu (whom Rajamanickam visited at the lodge), killed in his room. He chases a man who crossed him on his way up, but loses him.
Focus then shifts to John Britto, a missing man, who stayed with Raghu. Interviewing Britto's brother, he finds that Britto was the cause of disgrace to Dr Purushothaman (Y. Gee. Mahendra) and his family, who all committed suicide the previous September. JK gets permission to reopen Dr Purushothaman's case. Dr Purushothaman had been charged of bribery and his wife Annapoorni (Lakshmi), of instigating a lab attendant, Manikandan, to have sex with her. However, everyone questioned have only nice things to say about the family while Manikandan is said to be a scoundrel. It is found Manikandan has been missing since November.
Introduce the green Qualis which prevents an auto-driver from kidnapping a drugged woman and takes him in instead.
Tamilselvi while looking at old case records of the Purushothaman case, finds that Purushothaman had a daughter Suja who disappeared on the same day JK's sister did – September 6. JK investigates Purushothaman’s house and later goes to get details from a dodgy inspector, Isakki Muthu (G. Marimuthu), who handled the Purushothaman case. JK leads Isakki Muthu to give him details about Dorai Pandi (Manicka Vinayagam), a textile shop owner who was accused of peeping at girls in the change room of his shop through a hole in his office (one of whom was Suja).
JK then interviews Dorai Pandi who was able to get off after his manager Nadhamani took the blame. JK is unfazed and undeterred by what Dorai Pandi has to say and concludes the case is showing resemblances of having the Rashomon effect.
He then reconfirms again with Judas on the Purushothaman autopsy. He is able to get a major lead when he finds that there were two people in the auto that took Suja from her dance class. The same is established for his sister's disappearance.
We then find that ACP Tirusangu (Selva), Isakki Muthu, Dorai Pandi, Sharif, Inba (Yugendran), Raghu's murderer and the missing men – Nagoo, Moorthy and Rajamanickam are in cahoots. Tirusangu arranges for a few men to deal with JK and keep his nose out of their business. At this time, Sharif is kidnapped by the same Qualis. JK deals with the men (Intermission) and Sharif is executed but not before he names a few men.
A new box appears in a club used by two of the named and Sharif's head, with the eye-lids cut-off is found outside Isakki Muthu's police station. JK triangulates all misdeeds to the ACP and Isakki Muthu. But his boss Chandramouli (Aadukalam Naren) refuses to have the officers questioned fearing higher pressure. Unable to take any further action, JK requests a gun permit.
We then find that JK's sister (Iniya) is being held captive by Tirusangu. It is discovered she is the woman from the first scene. He plans to use her for later. Then, the Qualis comes again and tries to kidnap Isakki Muthu but is forced to flee when JK intervenes. Tirusangu realizes that someone is looking for revenge for Purushothaman's death and with the help of Purushothaman's ex class-mate, finds out whom. Both Tirusangu and JK then find that Purushothaman's family may not be dead. At a party, Judas comes in and tells Dorai Pandi & Co. (the men named by Sharif) that he is willing to sell information about their activities. He leads them to a van where they are gassed in. But while leaving, a shootout takes place between Tirusangu and JK, in which Judas dies after confessing.
Tirusangu & Co., organize “peep shows” with young girls for Dorai Pandi and others who are impotent. Suja (Srushti Dange) is one such victim (the girl in the auto). It’s during her incident that JK’s sister is also apprehended. Unable to bear this, she commits suicide. Her parents and Judas decide to take revenge on all those responsible. They fake their death after meticulous planning. They kidnap John Britto and then the peon Manikandan and make them confess. Auto-drivers Nagoo, Moorthy, and Rajamanickam were then kidnapped, tortured, and their arms amputated.
The boy Nishanth (Sunil Choudhary), is caught in the fracas and taken in. JK receives a call from Tirusangu's lot who want to trade his sister Charu for the boy. Chandramouli refuses to do so. However, his subordinates, Prakash, Tamilselvi, and constable Kitappa (E. Ramdoss), bring the boy to JK at the cost of their jobs.
Nishanth reveals the location of his parents as the old Binny Mills. Both parties head there. Another shoot out occurs. Nishanth is caught by Isakki Muthu but, is distracted by the arrival of a blinded Dorai Pandi & Co., and also John Britto and Manikandan, both with their tongues cut-off. Purushothaman and Annapoorni rush out and attack Isakki Muthu. Irrespective of how many times they are shot, they continue their onslaught, killing Isakki Muthu and the others of the gang, one by one. Finally, Tirusangu arrives with JK's sister. Seeing her as their daughter Suja, and this as a chance to save her life they sacrifice themselves for her as JK kills Tirusangu.
Dorai Pandi is sentenced for 13 years and the others 6-7 years. John Britto and Manikandan are given 3 years, JK & Co. are suspended. Nishanth is asked to be produced in court but JK sends him abroad as Mahesh Muthuswamy, giving him Viktor Frankl’s ‘Man's Search for Meaning’, asking him to reflect on his parents’ actions.Cheran as J. Krishnan (J.K.)
Dipa Shah as Thamizhselvi
Y. Gee. Mahendra as Dr. Purushothaman
Lakshmi Ramakrishnan as Annapoorni Purushothaman
Jayaprakash as Dr. Judas Iscariot
Selva as Trisangu
Manicka Vinayagam as Duraipandi
G. Marimuthu as Esakki Muthu
Shankar as Prakash
Yugendran as Inba
Aadukalam Naren as Chandramouli
Iniya as Charu
Sunil Choudhary as Nishant
Srushti Dange as Suja
Charulatha Mani (cameo appearance)
Neetu Chandra (special appearance)
Ameer Sultan (special appearance)
Charu Nivedita (special appearance)
Based entirely in Chennai, Yuddham Sei shoot was completed within 50 days.
Made on a budget of ₹4 crore, Yuddham Sei was a commercial success.
The Times of India gave 4 stars out of 5 and wrote, "With its apt casting and superb performances and direction, Yuddham Sei carries all the weapons needed for it to win its battle at the box-office". Rediff gave 3 stars out of 5 and wrote, "Yuddham Sei may have its flaws, but Mysskin's neat touches of situational humour, clever twists in the first half and convincing characters make this a neat film, if not a classic".
Sify called the film "average" and wrote, "the film has a few gripping moments but suffers on account of inconsistent writing which makes it drag in the second half". The Hindu wrote, "Mysskin is a thinking director, who makes no bones about his yen for makers in the league of Kurosawa and Kitano. The influence is generally seen in his intelligent storylines. Yet the first half of YS hangs in strands and confounds the viewer — ambiguity rules the segment. Nevertheless, the latter half brings you to the edge of your seat, most of the time". IANS gave 3 stars out of 5 and wrote, "Despite slow second-half, the films does impress as a smart and realistic detective story". Behindwoods gave 2.5 stars out of 5 and called it "A slow paced well made thriller". Deccan Herald wrote, "Stylised camerawork, haunting score and decent performances keep one interested, though the film is pulled down by its own weighty expectations. Still, Yuddham... is worth its while and wallet". Indiaglitz wrote, "Yudham Sei is absolutely watchable just for Mysskin and his way of story telling".