The evil Professor Klon (Aznil Nawawi) is back. This time, not only to overthrow the government and become the President of Metrofulus, but also to control the world's supply of fresh water through his ingenious plan; "Black Planet". When our blue planet has only 72 hours before turning black, Cicakman (Saiful Apek) comes to rescue.
But much to his surprise he face his old enemies; Ginger Boys, who return even more powerful as spiritual form as Ginger Ghosts (Adlin Aman Ramlie & AC Mizal). In addition, he is now faced with Professor Klon's hired assassin; Rrama (Tamara Bleszynski), an assassin who derives pleasure in killing as if it were a pure art form. As the situation starts taking a downward spiral, even a super hero needs help. But help appears in the most unexpected forms, including Danny (Yusry Abd Halim) his demised best friend, a powerful feng shui master, Miss Chee (Louisa Chong) and an unlikely party.
Apart from his heavy responsibilities to save the world, he also has his own personal dilemmas to address; that is Hairi vs Cicakman. He has to resolve his personal feelings towards Tania (Fasha Sandha), who is seeking the true identity of Cicakman and he also has to choose whether to sacrifice his own life or save Iman (Sharifah Amani), Danny's blind sister