Originally thought to have killed Stephanie by purposeful lack of medical attention, Dr. Thompkins actually faked Stephanie's death and set her up with a new identity in Africa to protect her. Stephanie, however, eventually insisted on going back to Gotham.
This was revealed in Robin #174.
The Robin/Spoiler Special showed that the two had spent Steph's "missing years" vaccinating small African villages and had grown very fond of each other. However, Stephanie jumped into a makeshift costume to save the village from a gun toting fanatic named Katavi who managed to shoot Leslie in the side. Stephanie rushed Leslie to a hospital and saved her life, but decided to go back to Gotham and keep being the Spoiler afterwards, realizing she couldn't change who she was. She told Leslie she "could never repay her."
Leslie is currently back in Gotham and running her own clinic, with paralyzed former Teen Titan Wendy Harris in her care.
When Ra's Al Ghul targeted people Bruce Wayne loved, he went after Leslie first. Tim Drake managed to stop the thugs from stealing Leslie's files, and Stephanie insisted on coming along to save Leslie. Tim had to admit he needed Stephanie's help.
Tim grabbed a dress for Stephanie so she could attend the ball Leslie was going to, and Steph "cut in" between Leslie and Wendy. After she led Leslie away, she told her there were assassins after her, to which Leslie responded, "Interesting lives we lead". Leslie insisted she could take care of herself, but Steph told her normally she'd agree, but Tim had really dragged something in on his shoe with this one. She urged Leslie to hide, and Leslie obeyed with encouragement of "Give 'em hell!"
Tim and Steph handily defeated the assassins, and afterwards, Leslie gave Steph her cell phone, saying there was a call form "her friend" (meaning Oracle) saying their communication systems were back online thanks to the note Steph sent about it.
This all happened in Batgirl (third series) (8).