If you want to dive Borneo, Sipadan is the "must go" dive destination. It's not as good as before, but still good. Just a heads up, you may see a lot of mainland Chinese tourists there. There isn't any pelagic diving in Sipadan, the chances of seeing whale shark is very rare. The Barracuda vortex (it's what makes Sipadan famous) is very very rare now. In Sipadan, school of jack fish is quite common, so is bumper head parrot fish. White/black tip sharks are common too, turtle is almost everywhere, in one dive I saw 10 turtles.
If you want to dive in Sipadan, the budget dive operator to use is "Seaventure", they're oil rig turned into dive resort, they have dormitory for people who're on the budget, the food is great. One thing you have to know is when you dive in Sipadan area, you only go to Sipadan 1 or two days, the rest of the trip are diving in Mabul/Kapalai, which is sandy bottom and mostly for macro stuff.
I also recommend switch things up, go dive with "Scuba Tiger", they're budget dive operator in Semporna area, which is 30 minutes away from Sipadan/Mabul/Kapalai. They have dive package that will bring you to east side of Borneo such as Bohey Tulang, PomPom island etc. These area are more for macro diving, but the beach and water are gorgeous. If you stay with Scuba Tiger, food is not included, you have to go eat at a cafe near by, or go to town to buy your own grocery. They have laundry facility, so it's a true budget place.
I came back from my Borneo/Sabah trip in March, here is the video that I made:
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