The story starts with floods at Ranga Saipet in Warangal District. Houses, trains, and people inundate in floodwater. A young man named Siddharth and his friends save the people up to their maximum effort. Eight of his friends assist him in the rescue. On the other hand, the Chief Minister recommends the candidature of Parakala Pappu Yadav for Assembly Elections. Pappu Yadav is a goonda who wishes to earn big through politics and power. To get the attention of people, he announces a sum of Rs. 5 crore for flood victims. The food that needs to reach the victims of the flood is taken elsewhere to be sold, an illegal way of earning money and backing up the flood relief fund into the pockets of the politicians. Siddharth learns of this through one of his friends and saves the stock in time. He then takes it to the flood victims for distribution. This annoys Pappu Yadav, for which Mondi Nani, his right-hand, threatens Siddharth. A strife develops between Mondi Nani and Siddharth, and the latter declares that his friend Ajay Kumar will be contesting the next Assembly Election opposite Pappu Yadav. Siddharth and his team get accolades from the people for this decision and start campaigning. To cut the good name of the group in the people and to win sympathy, Pappu Yadav conspires for a bomb blast allegation on Siddharth and his team. Mondi Nani works for him and the mission is accomplished. Pappu Yadav declares Siddharth and his team as terrorists. He wins the election, becomes the Home Minister, and his marriage is settled with Varalakshmi. Siddharth, with the help of many college students, kidnaps Varalakshmi from the marriage hall, demanding that Pappu Yadav state his crimes before a court of law. Varalakshmi is handcuffed and gagged with tape. The rest of the film shows Pappu Yadav chasing Siddharth to get Varalakshmi back while Siddharth and Varalakshmi fall in love while she is held captive. Finally, Siddharth puts an end to the game of crooked politicians.
Sainikudu has six songs composed by Harris Jayaraj. The music was released simultaneously in 10 venues from five countries – India, USA, Australia, Singapore and Dubai on the morning of 21 October 2006. The producer of the film, Ashwini Dutt, arranged the use of a satellite transmission to relay the live audio release across the globe. The music proved to be extremely successful upon release.