Timothy Zahn tells us that Emperor Palpatine's final dying thought after Vader hurled him down the energy shaft at the end of Return of the Jedi was to "Force-broadcast" to his Hand the command to "Kill Luke Skywalker." Why kill Luke and not the man who had murdered him? Who knows? Maybe ol' Palpy knew Vader's time was up. Maybe it was all a plot device for the books. In any case, Mara heard these instructions and witnessed, in a first-hand, Forcey-sort-of-way, her master's death. This was incredibly painful for her, and her hatred of Luke Skywalker was instantly solidified.

It took her many years to find Luke Skywalker (which we have to wonder about as well. Wasn't he carried around the GFFA on everyone's shoulders when they won the Battle of Endor? How hard can it be to find the guy?) but when she did find him, she tried to kill him. Numerous times. Unsuccessfully.

Over the course of Zahn's Heir to the Empire series, Mara realized that she no longer needed to follow the mutterings of her long dead evil overlord, and that she could build a life for herself in this brave new galaxy that did not entail being in the service of some Sith Lord or another. She and Luke had some adventures together (where she could have easily killed him a dozen times over but didn't, due to his skills and her seeming ineptitude), and so we leave the Zahn books with her and Luke as "sorta-kinda friends."