Why?
Contrary to popular belief at the time, the attack wasn't marking the beginning of an invasion. It was actually a tactical method. The Japanese were getting prepared to invade Timor and they didn't want any possibilty that Australia would counter-offend their attack. Therefore, they went to destroy the main military facilities in Darwin, which was the biggest contributing place in Australia for military services. Also, the Japanese would gain power of the seas that surround Australia.