Naya Ajooba (Athisayan) is about Devan (Master Devadas), who is sort of a child prodigy, with a computer-like mind and very good in studies and extra-curricular activities. R. C. Shekhar (Jackie Shroff, a scientist, lives very near their house, with his servant Damodaran (Harisree Ashokan). He is working on a project, which could help in making human beings invisible. On the very day that he successfully experiments his 'magic' potion on a rabbit, he is urgently called to the U.S as his daughter, who is studying there, meets with an accident.
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Meanwhile Maya's friend and lover Roy (Jayasurya), who too had been a journalist, is in jail after having been framed in a murder case by some influential politicians including the State Revenue Minister Divakaran (Rajan P. Dev), another minister Yunus Kunju (Ramu), the Police Commissioner Shanmughan (Bheeman Raghu) and the very influential Kuwait Nazar (Devan). With the help of the newly appointed Collector Anita Williams (Karthika), Maya shoots a video of these baddies accepting millions of rupees as commission from some Arab businessmen, who are there to sign some business deals with the State Government. Maya immediately goes to Radharamanan and shows him the clip. Radharamanan is thrilled and agrees to telecast it, after discussing it with the Board of Directors. Somehow Nazar, Divakaran and others come to know of this and they go after Maya, in order to get from her the memory card containing the clipping. On the very same day that R.C.Shekhar goes to the U.S, Maya is abducted by Nazar and group. The kids are baffled. Anita Williams, Father Chanthakkadan and Radharamanan know who are behind this, but nothing can be done without sufficient evidence. And then Devan, who had seen R.C. Shekhar conducting the experiment on the rabbit, steals into Shekhar's lab and drinks the potion. He becomes invisible and sets out to save Maya.
Devan did manage to save Maya, but due to the medicine overdose, he turns into a gigantic monster and has to leave Maya and the children and makes his abode in the deep ocean.