The dreadful story of Pakshi Rajan!

Dr. Vaseegaran has recently built a new android humanoid assistant named Nila, whom he introduces to a group of college students. Shortly after, all the mobile phones in the city begin to fly into the sky, throwing the public into a panic. A scientific council assembles to discuss the phenomenon, in which Vaseegaran suggests reactivating the robot Chitti. But the plan is opposed by a member of the council, Dhinendra Bohra, whose father was killed by Chitti a few years back.

The cell phones gather into a swarm and kill phone retail store owner Jayanth Kumar, telecom company owner Manoj Lula, and Telecom Minister Vaira Moorthy. The Home Minister S. Vijay Kumar gives permission for Vaseegaran to reactivate Chitti, whom he has already started working on. The cell phone swarm destroys phone towers around the city and wreaks havoc on the public, manifesting as a giant bird. A newly activated and upgraded Chitti battles the bird in the city and destroys it with an explosion. The remaining phones retreat and reform. Chitti, who runs out of battery takes refuge in three antennas at a space station. The bird tries to follow but is repelled by the antennas.

Chitti informs Vaseegaran about this incident and confirms that the phones are powered by an aura, specifically a concentrated mass of negative charge with electromagnetic properties. Since the space station was streaming positive charged ions into space, the bird was repelled. Vaseegaran builds a photon synthesizer that projects positive charge, intending to neutralise the charge of the bird. The group confronts the bird and drains it of power. The phones take up a humanoid form, as the deceased ornithologist Pakshi Rajan.

Chitti converses with Pakshi as he attempts to destroy the synthesizer, in which a flashback reveals that Pakshi protested against the usage of modern mobile phones, from which the radiation affected the brains of birds and caused mass deaths, especially near his bird sanctuary and home in Thirukazhukundram. Pakshi makes conferences and protests to address this, but the public dismisses and mocks him. Lula and Moorthy also reject his morals for their business and Jayanth Kumar shuns him from his shop as he tries to protest. Birds all over the city including Pakshi's sanctuary die out, including newborn chicks. A distraught and angered Pakshi, after even a court investigation found no violations (because telecom companies reduced signal levels to conceal wrongdoing), hangs himself at a cell tower. Pakshi's negatively charged spirit reawakens by the radiation emitting from the tower. By absorbing the souls of all the deceased birds in the city, he becomes a vengeful entity.

Chitti tries to convince Pakshi not to hurt the public but Pakshi wishes to punish their ignorance. Chitti has Pakshi captured and contained. The news spreads to the council which decides to build an army of such robots for the military. Dhinendra, who becomes angered by Chitti's victory, releases Pakshi's spirit from the synthesizer. Pakshi possesses Vaseegaran and attacks the public again, but Chitti refuses to attack his creator. Nila gets the red chip and reprograms Chitti to his evil 2.0 alter ego, after altering it to not harm the innocent and commanding him only to fight Pakshi.

Pakshi traps 80,000 people in a football stadium and kills Dhinendra, who was present, by focusing radiation from multiple cell towers. Chitti interferes and fights Pakshi's bird form with his army. As Chitti runs out of charge, Pakshi turns into his winged form and creates several bird drones. The drones tear the robots into pieces, but before Pakshi can summon radiation he's interrupted by one of Chitti's creations: the action figure bot Kutti 3.0. Released into the stadium by Nila, the Kutti bots mount themselves on doves, forcing Pakshi to stand down. The Kuttis self-destruct and destroy Pakshi's drones. After Vaseegaran is released from possession, Pakshi is led to the space station where he is destroyed.

Vaseegaran recovers in the hospital and tells Vijay Kumar, who comes to see him, that he feels Pakshi Rajan was a virtuous person who became a victim of the corrupt society. He also suggests we reduce and control cell phone radiation and ensure that technology do not threaten the lives of all the living creatures in the world. Chitti, now restored to its original version, begins a relationship with Nila.

Sana asks Vaseegaran over the phone about the probability of mobile phones flying again. Immediately, Vaseegaran's mobile flies out of his hand and morphs into Kutti 3.0, saying, "I am your grandson"