THis has always been my theory
Natalee was on the beach late at night with Van Der Sloot, both having had too much to drink. He wanted to be intimate, she didn't and when he got a little too handsy, she tried to run away. He got up, caught her, slapped her around, raped her and in the middle of it, got a little too physical with her, killed her. He panicked, called his dad who instructed him on how to dispose of the body. He and the Kalpoe brothers took the body to a boat, took her a mile or so out to sea, probably cut the body a little to produce blood and dumped it. Needless to say, the body was quickly eaten by sharks.
I hate to say it but I don't think we'll ever know, despite the fact those little turds know what happened to her.