One of the last missions the Emperor assigned her to was the killing of Luke Skywalker. The Emperor claimed to have foreseen her involvement in Luke's death, and sent her to Tatooine following Vader's failure to capture Luke at CloudCity. She infiltrated Jabba's palace as a dancing girl, but was not allowed onto Jabba'ssailbarge when it left to sacrifice Luke and Han to the Sarlacc. This unfortunate setback allowed her to continue in her efforts to kill Luke, but the death of the Emperor at Endor robbed her of her Force abilities and her main source of impetus.
She went underground after Palpatine's death, since - as a secret agent for the Emperor - none of the surviving Imperials would ever believe she was more than a dancing girl. She performed a number of odd jons across the galaxy before she joined up with Talon Kaarde. She was working on Tropis at the time, and was employed by two safari hunters who turned out to be Talon Kaarde and TapperQuelev. When Kaarde and Quelev got into trouble, Mara intervened and helped Kaarde escape. They then made proper introductions, and Mara asked for a job. She joined up just before he became involved with the NewRepublic, and was once again thrown into Luke's path. The Emperor's command to kill Luke resurfaced, but the events surrounding Grand Admiral Thrawn's plans for Luke and the NewRepublic kept getting in her way.
She found herself helping Luke more often than not. When she and Luke were reunited in C'baoth's stronghold on Wayland, she fulfilled her "destiny"; to kill Luke Skywalker, but not in the way she or the Emperor had forseen. When C'baoth sent a clone of Luke to battle the original Luke, Mara destroyed the clone. Following the death of Grand Admiral Thrawn Mara worked with the NewRepublic as a liaison between the Republic and the newly-formed Smugglers' Alliance.
Following the death of the reborn Emperor on Byss, Mara continued to assist the Republic, but was increasingly pursued by LandoCalrissian, both on a business level and a personal level. She kept Lando at arm's-length from a personal standpoint, but joined in with him to restart the Spice Mines of Kessel as a legal source of glitterstim spice. They were also employed by Talon Karrde to search out the location of JorjCar'das, a job which took them nearly six years to complete on the side.
During the Caamas Incident, Mara took a group of Karrde's people to Nirauan, to search out the strange ships that attacked them in the Kauron asteroid field. She was stranded on the planet, and was eventually rescue by Luke. They realized that their relationship was now stronger than ever, especially after Mara bluntly showed Luke that his use of the Force needed to be minimized before he could fully understand it. Luke, in response, helped Mara realize her potential with the Force, unlocking it in time to use it to escape from the Chiss who controlled the Hand of Thrawn. During their escape, Luke asked Mara to marry him, a question to which she immediately agreed.
After the resolution of the Caamas Incident, they were wed: once, in a solemn Jedi ceremony performed by KamSolusar; and again in a public ceremony on Coruscant. Both agreed that they should travel the galaxy as Jedi instructors, leaving the JediAcademy on Yavin 4 to grow beyond Luke's vision.
A few years later, Mara suddenly became ill. Through the sheer will of the Force, she remained active, but was unaware that her illness was actually engineered by Nom Anor, in an attempt to see just how powerful the Jedi Knights were. She resisted the disease he had created long after other victims were dead and buried. After the creature named Vergere escaped from the Millennium Falcon and her servitude to the YuuzhanVong priestess Elan, Han Solo returned to Coruscant with a sample of Vergere's tears. The creature claimed they could help heal Mara's disease, and Mara was more than willing to try. The initial stages of her recovery were somewhat painful, but whatever Vergere gave them drove off the disease. She hesitated to call herself cured, and retained a small portion of the tears for later use.
Soon after the Battle of Fondor, Mara discovered two momentous things: first, that it was Nom Anor who had poisoned her on the planet Monor II; and second, that she was pregnant with Luke's son. She refused to stop fighting against the YuuzhanVong, but also realized that she could not longer be at the forefront of the fight. When the Senate ordered Luke's arrest, the couple set out for the Errant Venture, where Mara struggled with her pregnancy. It had been complicated by toxic shock syndrome, brought on by the use of Vergere's tears. With Luke's devotion to her and his connection with the Force, he drove out the YuuzhanVong disease and helped Mara give birth to a son, Ben.
Luke and Mara spent less time with Ben than they had hoped to, when they were pressed into action defending the Eclipse base from invasion and, later, defending Coruscant. With the fall of Coruscant, Ben was separated from them, but was kept safe by Leia Organa Solo and her husband, Han. Mara and Luke then set out on a most dangerous mission: to locate the rogue planet ZonamaSekot. They were escorted by ArienYage and the Widowmaker after lending assistance at the Battle of Bastion, and eventually located the mobile planet in the KlasseEphemora System. Although the planet initially refused to help them, the actions of Luke and the Jedi Knights later convinced Sekot that they were searching for a peaceful resolution to the war against the YuuzhanVong. The planet then agreed to follow them back into the galaxy and assist them in any way possible.