The central objective of the Eternal Alliance at Nathema was preventing the Order of Zildrog from initiating the awakening of the machine god Zildrog, known as Iokathi, on the planet Nathema. After discovering Zildrog's whereabouts, the Alliance received an encrypted message from their secret operative, Theron Shan, which directed them to an Abandoned Listening Post. There, they uncovered details regarding the Order's history and their underlying reasons. Based on the intel provided by Theron Shan, the Alliance Commander and Lana Beniko journeyed to Nathema, where they were reunited with Shan, who assisted them in their attempt to thwart the Order. Despite overcoming the Order's defenses and reaching Zildrog's location beneath an ancient Sith Temple, they arrived too late to prevent Zildrog's reawakening. Confined within a force field generated by GEMINI 16, they were helpless witnesses as Zildrog's true form was revealed: the Gravestone itself. The Alliance's most important asset, stationed at Odessen, was seized by Zildrog, who then employed its omnicannon to completely annihilate the Eternal Fleet. As Zildrog prepared to target Odessen, the Alliance leaders seized the opportunity to engage and eliminate GEMINI 16, defeat Vinn Atrius, and ultimately destroy Zildrog. However, this final act also triggered the Gravestone's self-destruct mechanism and disabled the Eternal Throne, resulting in the loss of the Alliance's most valuable military resources and prompting many members to abandon the cause.

Theron Shan acquired information from a holomap belonging to the Sith Emperor on Copero, which he then transmitted to the Order of Zildrog. This revealed the location of the ancient machine god Zildrog on Nathema, a planet where the Force had returned following the death of Vitiate. Subsequently, the Order relocated their operations base from an abandoned listening post to Nathema, assigning Shan the task of erasing all data. However, Shan, secretly loyal to the Eternal Alliance, created encrypted data backups and sent a message containing the word "Zildrog" to the Alliance.

The Alliance Commander and Lana Beniko discovered this message and decided to investigate personally. Upon arriving at the listening post, Lana and the Commander viewed holomessages that exposed the Order's key members and their motivations. The final data entry before their arrival included coordinates on Nathema, encrypted using a unique method developed by Theron and Lana on Rishi during the Revanite crisis. After the self-destruct mechanism was activated, completely destroying the station, Lana and the Commander were forced to escape. They returned to Odessen as the restoration of the Copero holomap was completed, confirming the validity of Theron's information.

Lana and the Commander departed for Nathema aboard a shuttle to intercept the Order, while Hylo Visz mobilized the Eternal Fleet in orbit around Odessen. Meanwhile, the Order, aided by allies seeking personal revenge against the Commander, had unearthed Zildrog within the ruins of an ancient Sith Temple. Lana and the Commander landed on Nathema and proceeded towards the coordinates, battling Nathema Zealots and creatures that had escaped from the destroyed Sanitarium. Simultaneously, Theron deserted the Order and rejoined them at the designated rendezvous point, where he confessed his true allegiance and sought their understanding and forgiveness.

The trio then hurried to halt the Order, but GEMINI 16 detected their presence and initiated the ritual to awaken Zildrog prematurely, while another member of the Order dispatched an Ancient Guardian Droid to confront the Alliance. The GEMINI deceived and betrayed some of their allies, imprisoning them within energy transfer chambers to fuel Zildrog's awakening. After descending into the Verdant Valley, the Alliance reached the temple and overcame the machine, subsequently entering the temple itself. They arrived at Zildrog's location just in time, and Theron Shan immediately shot [Vinn Atrius](/article/vinn_atrius]. GEMINI 16 then trapped the three of them within a force field and revealed that the ritual was complete and Zildrog had awakened. Zildrog then exploited his connection to the Dark Sanctuary to remotely seize control of the Gravestone, which was stationed on Odessen.

Zildrog maneuvered the Gravestone into orbit around Odessen and proceeded to obliterate the Eternal Fleet with its omnicannon. Zildrog then targeted Odessen itself and initiated a recharge sequence before the next attack. However, back on Nathema, this action deactivated the force field, compelling GEMINI 16 to directly engage the Alliance. Lana, Theron, and the Commander fought and destroyed the GEMINI droid, and Theron attempted to shut Zildrog down, but was suddenly stabbed in the back with a lightsaber pike by Vinn Atrius. Driven by vengeance, Atrius commanded Zildrog to amplify his power, after which he attacked Lana and the Commander with his newfound strength. The two defeated Atrius and destroyed Zildrog, but this final act also triggered the Gravestone's self-destruct and disabled the Eternal Throne. The Commander determined Atrius' fate, while Lana tended to Theron's injuries, recognizing that he needed immediate medical attention on Odessen.

Hylo Visz dispatched a shuttle to retrieve them, and upon their return to Odessen, Lana informed the Commander that Odessen had sustained minimal damage with no casualties among Alliance personnel. Nevertheless, the Gravestone and the Eternal Fleet, two of the Eternal Alliance's most potent weapons, were lost, eliminating any advantage the Alliance held over the Republic and the Sith Empire, who intensified their preparations for a renewed open conflict. Furthermore, with the Alliance's original objective of overthrowing the Eternal Empire accomplished, many of its members chose to depart and rejoin their respective factions. Despite formal apologies from factions associated with the Order of Zildrog, this setback demonstrated the Eternal Alliance's vulnerability, prompting Lana and the Commander to seek potential allies for the upcoming conflict. The new government of Zakuul also seized this opportunity to sever ties with both the Alliance and their former colonies, establishing itself as an independent world.

The events are portrayed in "The Nathema Conspiracy" flashpoint, released with the corresponding Update. During the mission, the identity of the individual who confronts the player before the Ancient Guardian Droid fight varies based on the player's class, alignment, and previous choices, with each class encountering one of two possible antagonists related to their class story. Similarly, the identities of the other two victims used to awaken Zildrog depend on the choices made during the Knights of the Eternal Throne expansion.
At the flashpoint's conclusion, players can choose light-side options to either imprison Vinn Atrius or return him to Zakuul for his people to handle, or execute him on the spot using a dark-side option. The player must then either abandon Theron Shan to die in a dark-side option or transport him back to Odessen for healing in a light-side option. The latter is followed by a neutral choice to either welcome Theron back into the Alliance or permanently exile him.