The confrontation at the Lake of Apparitions unfolded between Luke Skywalker, the Jedi Grand Master, the heretical Dark Lord of the Sith known as Darth Krayt, and the dark side entity called Abeloth. This event transpired on Abeloth's planet during the year 44 ABY. Following Abeloth to the Maw were Luke Skywalker and his niece, Jaina Solo, recently elevated to the rank of Jedi Master. Abeloth had abducted Skywalker's son, Ben, alongside the Sith apprentice Vestara Khai, holding them within the meditation sphere known as Ship.
When Ship launched an assault on Luke and Jaina's vessel, the Rude Awakening, Luke ventured into the realm of beyond shadows to seek assistance from the spectral form of his wife, Mara Jade Skywalker. It was there that he encountered the Dark Man from his visions of four years prior, who was actually Krayt. Krayt joined him in the ensuing struggle against Abeloth.
After the Rude Awakening came under attack by the Sith Meditation Sphere named Ship, Luke Skywalker secured himself within a medbay and journeyed to beyond shadows. His arrival point was the Lake of Apparitions, which he traversed until he located the spirit of his wife, Mara Jade. Luke implored Mara for any insight she could offer on defeating Abeloth, but she possessed none. Subsequently, the spirit of Jacen Solo materialized.
Initially, Jacen voiced his disappointment with Luke for attributing Abeloth's escape to his nephew. However, his disapproval dissipated when Luke clarified that Jacen's attempt to alter his vision within the Pool of Knowledge had inadvertently facilitated the entity's liberation. Despite their efforts, Mara and Jacen remained unable to provide assistance. It was then that the Dark Man made his entrance. This newcomer was, in reality, Darth Krayt, the Dark Lord of the Sith and leader of the clandestine heretical sect known as the One Sith. Without disclosing his true identity, he informed Luke that he was a Sith and that his purpose was to aid Skywalker in vanquishing Abeloth.
At that precise moment, Abeloth emerged from the Mists of Forgetfulness. The Grand Master attempted to summon his lightsaber, but being beyond shadows, he found himself without one. Luke then tried to strike Abeloth with Force energy, but she countered with a torrent of Force lightning that bypassed Krayt and struck the Jedi.
Upon regaining his composure, the two began to bombard Abeloth with blasts of Force energy until she began to sink into the Lake. During this confrontation, Luke's perception of time became distorted, causing what felt like an eternity to pass in what might have been a mere instant. As Abeloth teetered on the brink of falling into the water, Luke rushed to her side and initiated a physical assault (or what approximated physicality beyond shadows – the conflict was between their Force essences, precluding any physical harm). Luke began to gain the advantage over Abeloth, and the two grappled as Abeloth's tentacles whipped across Luke's face. One of her tentacles struck Luke in his right eye, causing blindness in that eye. Krayt then entered the fray, plunging his fingers into Abeloth's abdomen, resulting in a burst of black fluid. As the three tumbled across the Lake's surface, Abeloth attempted to repel Krayt with a Force blast, but her efforts proved futile.
Abruptly, Krayt turned against Luke and Abeloth, employing a Force draining technique to siphon their powers. In response, Luke struck the Sith's knee and dislodged him from the other two, sending him crashing onto the Lake's surface. Luke threatened to release Abeloth if Krayt persisted, and Krayt relented despite his initial defiance. Luke maintained his grip on Abeloth as Krayt continued to drain her for what seemed like days, only for it to feel like mere seconds as the Sith began to cry out in agony. Dark, shimmering Force energy began to emanate from Krayt's wounds, spreading across the Lake in a boiling, oily slick that caused the water to steam and hiss. Luke realized that Krayt had not betrayed him; the act of restraining Abeloth was taking as much from Luke as the draining was from Krayt.
Seizing the opportunity, Abeloth tore her head free of Luke's grasp and attempted to seize anything within reach with her teeth. However, Luke restrained her in a chokehold, intensifying his connection with the entity as he urged the Sith to continue. As Krayt persisted, Abeloth retaliated, sending the three of them spiraling across the Lake's surface. Even amidst their chaotic movements, Krayt maintained his grip on Abeloth's chest, despite the continued flow of black Force energy from his wounds. As they rolled, Abeloth appeared to be guiding them toward the shore, prompting Luke to propel them back toward the Lake's center by pushing off a rock. At that moment, Abeloth vanished, taking Krayt's hand with her, leaving Krayt's severed arm pointing at Luke and now draining energy from the Grand Master. Once again suspecting Krayt of betrayal, Luke prepared a Force blast, but Krayt halted his assault and directed his arm toward the edge of the Lake, near the Mists of Forgetfulness. Abeloth was retreating into the Mists, with Krayt's wrist still embedded in her chest and dark energy continuing to flow from the limb.
Krayt attempted to use the Force to retrieve his hand, but Luke deduced that she had only fled because she was dying and that her only recourse was to attack. She teleported back to the pair, plunging a mass of tentacles deep into Krayt's chest and then into Luke's as he attempted to intervene. Despite her attack, Luke maintained his offensive, grappling with her relentlessly until his elbow pierced through Abeloth's head. At that precise moment, Saba Sebatyne successfully eliminated Abeloth's avatar residing within the Jedi Temple's computer core. Simultaneously, near the Font of Power, Ben dispatched Abeloth's avatar, High Lord Korelei, with a shikkar. With the demise of her final two bodies and the annihilation of her Force essence, Abeloth met her end. Her body disintegrated, pulling the tentacles with it, and leaving Krayt and Luke clutching fragments of her essence. The two collapsed, the tentacles having left gaping wounds in their chests. Luke lost consciousness and began to scream, causing his physical body back on the Rude Awakening to echo his cries.
Upon awakening, Luke and Krayt observed Abeloth's body beginning to sink into the Lake of Apparitions as it diminished in size. With Abeloth's death, the Family of the Ones reached its conclusion – a process that had commenced nearly 65 years prior with the deaths of the Father, the Son, and the Daughter. Luke believed that by defeating Abeloth, he had permanently averted the rise of the Sith and restored the course of the Current of the Force, as the Thuruhts believed the Ones were destined to do. However, Jacen informed him that he had not prevented the Sith's rise, but had merely prevented Jacen's vision from materializing. Jacen also revealed the true nature of his vision within the Pool of Knowledge – the vision that had ultimately led him to embrace the dark side and become Darth Caedus: he had witnessed the Dark Man upon the Throne of Balance, but his attempts to prevent it were focused on his daughter Allana standing beside Krayt on the Throne.
Furthermore, despite Abeloth's demise, the New Jedi Order anticipated the potential for her return. Consequently, they dispatched Quest Knights to locate the Mortis monolith in order to retrieve the Dagger of Mortis, as a precautionary measure in case she did return, as a means to kill her for good.