For most visitors, the most common option for scuba diving is to fly on the Layang Layang chartered flight which operates several flights per day during the peak season from Kota Kinabalu. Check with dive resort for flight schedules. As of 2012, the flight costs precisely US$360 return, including taxes. Flight time is about one hour. In addition to the one resort on the island, there are at least two liveaboards that visit the island and sail from Kota Kinabalu.
The process is that you arrive at the KK International Air terminal in Kota Kinabalu about 5AM. Here you and your luggage are weighed. This is a particularly amusing thing to watch, especially when someone is over 100kg as the luggage scales max out. After a hour or two waiting around whilst luggage and food is loaded, the flight departs.
A few words of advice about the actual flight: Note that small freight planes are used. The largest can take about 20 people and you board through the rear cargo ramp. There is a lovely scenic view of the cargo plane interior - not every seat pair has a window, only the emergency exits. Given the humidity, when the aircon system starts during the flight, there is a lot of smoke-like mist which pours from the ceiling vents - this is not a cause for alarm but is enough to set off the nervous flyer! Spare seats are occupied by your dive bags and trays of eggs and onions. This all makes for an interesting flight - take a book.