at the end of the game on malachor V are you soposed to be fighting alone i heard that you should be with atton and the handmaiden at the verry end or did they die in the ebon hawk and if they did how did bao-dur just apear

In both ls and ds endings, I fought through the ending by myself.

You go through Malachor alone - see all the threads on Cut Ending stuff in the spoiler forum to find out about this sort of stuff.