In the year 2004 Shaji Kailas made a comeback in Malayalam with Natturajavu. With Mohanlal in lead role and, scripted by T. A. Shahid, Natturajavu was a disaster at the box office. In the year 2005 Shaji Kailas directed The Tiger, an investigative thriller starring Suresh Gopi. In 2006, Chinthamani Kolacase, another investigation thriller with Suresh Gopi in a leading role, was released.
However, his first film with Dileep, The Don, turned into a huge flop in 2006. The next film, Baba Kalyani, starring Mohanlal, was an average hit at box office. But later, Shaji failed to find his rhythm, resulting a series of huge flops in a row. Time in 2007, Alibhai and Sound of Boot in 2008 dead at box office. In January 2010, Shaji Kailas directed Drona 2010, which turned out to be another commercial fiasco. Beginning of 2011 showcased his attempt to reclaim his position within Malayalam industry with the sequel of yesteryear mega hit "August 1", 15 August which garnered heavy negative reviews from critics and audiences alike and was finally declared as another flop by Shaji Kailas. His next movie was with Mammotty and Suresh Gopi named The King and the Commissioner the movie was the next part of the yesteryear blockbusters The King and Commissioner.