Darwin does not show up directly in the website's booking page but if you click through to the route map, Darwin appears. From here it is possible to check bookings to Kuala Lumpur and beyond.
A return flight Darwin to Kuala Lumpur can be purchased today for 3,324 Malaysian Ringgit or about $1,147 Australian dollars. This over the top price is about the same price as internet agents like Kayak.com.
However, more reasonable fares may be just around the corner. The NT News reports that Malaysia Airlines will start selling from 28 July at a much more reasonable price of $479. The next best offering is a Virgin codeshare (Silkair) via Singapore at $602.