The duel at the Lake of Apparitions was a battle between Grand Master Luke Skywalker, Dark Lord of the Sith Darth Krayt, and the dark side entity Abeloth that occurred on Abeloth's planet in the year 44 ABY. Luke Skywalker and his niece, newly appointed Jedi Master Jaina Solo, had followed Abeloth to the Maw, where she had taken Skywalker's son Ben and the Sith apprentice Vestara Khai in the meditation sphere Ship.
Abeloth was attempting to recreate the Family of the Ones, who had died on the planet Mortis around 21 BBY, by making Ben and Vestara drink from the Font of Power and bathe in the Pool of Knowledge. When Luke and Jaina's ship, the Rude Awakening, was attacked by Ship, Luke entered the realm of beyond shadows to seek help from the spirit of his wife, Mara Jade Skywalker. There, he encountered the Dark Man of his visions from four years earlier, who joined him in battle against Abeloth.
When the Rude Awakening was attacked by the Sith Meditation Sphere Ship, Luke Skywalker strapped himself into a medbay and traveled beyond shadows. He arrived at the Lake of Apparitions, where he traveled across the Lake until he found the spirit of his wife, Mara Jade. He asked Mara for anything she could tell him about how to defeat Abeloth, but she had nothing—and then the spirit of Jacen Solo arrived as well.
Jacen was initially disappointed in Luke for blaming Abeloth’s escape on his nephew, but his scorn vanished when Luke explained that Jacen’s attempt to change what he saw in the Pool of Knowledge had resulted in the entity's freedom. Mara and Jacen were still unable to help him, but then the Dark Man arrived. The newcomer was in fact the Dark Lord of the Sith Darth Krayt, leader of the One Sith. Without revealing his true identity, he informed Luke that he was a Sith, and that he was there to help Skywalker defeat Abeloth.
At that moment, Abeloth arrived out of the Mists of Forgetfulness. The Grand Master attempted to reach for his lightsaber, but as he was beyond shadows, he did not have one. Luke then attempted to blast Abeloth with Force energy, but she had already unleashed a barrage of Force lightning that passed through Krayt and slammed into the Jedi.
Once he had recovered, the two began to pummel Abeloth with blasts of Force energy until she began to fall into the Lake itself. During the battle, Luke’s sense of time was warped, so what seemed like a lifetime could have been a blink of an eye. As Abeloth was about to fall into the water, Luke ran to her side and began to attack her physically (or what passed for physical beyond shadows–the combat was between their Force essences, and as such there were no physical injuries). Luke began to gain the upper hand over Abeloth, and the two began to grapple as Abeloth’s tentacles lashed Luke’s face. One of her tentacles hit Luke in the right eye, blinding him in that eye. Then Krayt joined the fight, jabbing his fingers in Abeloth’s stomach and causing a black spray to erupt. As the three tumbled across the surface of the Lake, Abeloth attempted to Force-blast Krayt off of her, but her efforts were in vain.
Suddenly Krayt turned on Luke and Abeloth, using a Force draining technique to steal both of their powers. In response, Luke bashed the Sith’s knee and threw him off the other two, dropping him to the surface of the Lake. Luke threatened to release Abeloth if Krayt did not stop, and Krayt consented despite his words otherwise. Luke held fast to Abeloth as Krayt continued to drain her for what seemed like days, but it suddenly felt like seconds as the Sith began to scream in anguish. Force energy, black and shiny, began to seep from Krayt’s wounds across the Lake in a boiling, oily slick that caused the water to steam and hiss. Luke realized that Krayt had in fact not betrayed Luke–the effort of holding Abeloth down was taking as much from Luke as the draining was from Krayt.Abeloth chose that moment to rip her head free of Luke’s hold and try to grab anything she could reach with her teeth, but Luke grabbed her in a choke hold and merged his presence even more with the entity as he told the Sith to keep going. As Krayt continued, Abeloth burst into action again, sending the three of them tumbling across the surface of the Lake. Even as they rolled, Krayt kept his hand buried in Abeloth’s chest despite the black Force energy still pouring from his wounds. As they rolled, Abeloth seemed to be directing them towards the shore, so Luke pushed off a rock and sent them tumbling back towards the Lake’s center. At that point, Abeloth simply vanished–taking Krayt’s hand with her–leaving Krayt’s stump of an arm pointing at Luke and now draining energy from the Grand Master. Once again believing Krayt was about to betray him, Luke prepared a Force blast, but Krayt stopped his attack and pointed his arm towards the end of the Lake, near the Mists of Forgetfulness. Abeloth was backing into the Mists, with Krayt’s wrist still protruding from her chest and dark energy still pouring from the limb.
Krayt tried to use the Force to pull his hand back to him, but Luke realized that she had only fled because she was actually dying–and that her only option now was to attack. She teleported back to the duo, slamming a ball of tentacles deep in Krayt’s chest and then Luke’s as well when he tried to help. Despite her attack, Luke continued to press the offensive, grappling with her mercilessly until his elbow simply pushed through Abeloth's head. At that very moment, Saba Sebatyne succeeded in killing Abeloth’s avatar that was inhabiting the Jedi Temple's computer core. Simultaneously, near the Font of Power, Ben killed Abeloth’s avatar High Lord Korelei with a shikkar. With the death of her last two bodies and the destruction of her Force essence, Abeloth died. Her body fell away pulling the tentacles with her and leaving Krayt and Luke holding pieces of her essence. The two collapsed, the tentacles having left gaping holes in their chests. Luke fell unconscious as he began to scream, causing his physical body back on the Rude Awakening to scream as well.
When Luke and Krayt awoke, Abeloth's body was starting to sink into the Lake of Apparitions as it shrank. With the death of Abeloth, the Family of the Ones finally met its end–a process begun almost 65 years ago, with the death of the Father, the Son, and the Daughter. Luke believed that by defeating Abeloth, he had prevented the rise of the Sith forever, and that he had restored the course of the Current of the Force, as the Thuruhts believed the Ones were meant to do. But Jacen informed him that he had in fact not prevented the Sith's rise–he had simply prevented Jacen’s vision from coming true. Jacen also told Luke what he really saw in the Pool of Knowledge—the vision that had ultimately caused him to turn to the dark side and become Darth Caedus: he had seen the Dark Man on the Throne of Balance, but what he had tried to prevent was his daughter Allana standing next to Krayt on the Throne.
In addition, although Abeloth had died, the New Jedi Order anticipated the possibility of Abeloth returning, so they dispatched Quest Knights to locate the Mortis monolith in order to retrieve the Dagger of Mortis, as a precautionary method in case she did return, as a means to kill her for good.