In 3643 BBY the Jedi Master Ngani Zho, who is now living as a vagrant recalls the Great Galactic War and the accomplishments of his former students—Satele Shan, Jaric Kaedan, Syo Bakarn, and Bela Kiwiiks—at the Battle of Rhen Var, where Shan led them and the Republic Army to victory and personally defeated the Dark Councilor Darth Mekhis. On Coruscant, Theron Shan—an agent of the Republic Strategic Information Service—interrupts a meeting between Black Sun and a Twi'lek smuggler named Teff'ith, whom Shan subdues after defeating the Black Sun thugs. Shan is called in by the SIS Director, who sends Shan on a mission to locate and retrieve Ngani Zho because he had reappeared near Imperial space after a decade of absence. Zho had raised Shan as a child after his mother, Satele Shan, gave him up to continue serving as a Jedi.
At the same time, Darth Mekhis—now scarred from her encounter with Satele Shan a decade prior—tests the warship Javelin Dreadnought and sends her Sith Knights to capture Zho. Theron Shan brings a captive Teff'ith along for the ride as he tracks down Zho on the planet Taris, but their reunion is disrupted by the arrival of Mekhis' Sith Knights. The two flee back to Shan's ship, and Teff'ith begrudgingly aids them in their escape to save herself from the Sith Knights; as they depart Taris, Shan questions Zho about his absence, and Zho has a mental breakdown as he tries to force Shan to take them to the Vesla system—one of the seven systems ceded to the Empire during the Treaty of Coruscant. Shan tranquilizes the crazed Jedi Master, and he then sets out for the shadowport of Port Nowhere to acquire the navigational data necessary to get to the Vesla system. The agent also recalls how Zho had been like his father, but how the Order had ultimately asked him to leave when it became apparent that Shan was not Force-sensitive.
On Port Nowhere, Zho and Teff'ith distract a smuggler in one of the ship's cantinas by offering to hire him while Shan hacks the smuggler's vessel and downloads the man's Imperial clearances and navigation charts for Imperial space. The trio then heads to the Vesla system, where Shan sets them down on one of the outlying planets and they spend the next few days constructing a spy ray to survey the inner planets and see what the Empire is doing in the system. With the spy ray, Shan discovers that the inner planets have been destroyed by various weapons technologies, and Zho's memories return completely as Shan identifies the Sun Razer: a massive space station around the system's sun that is siphoning the star's materials and energies to produce massive superweapons. However, the three are captured by the Imperial warship Valor Prevails before they can escape the system.
As Zho is tortured by the Sith aboard the Sun Razer, he relates how he went undercover as a slave to investigate the Empire's activity in the Vesla system after the Treaty. Zho had helped protect his fellow slaves from their Imperial overseers for many years, but his mind locked away his memories of the Vesla system after he witnessed the Empire test their new weapons—a test that killed almost all of the slaves who had helped to construct the Sun Razer—and Zho had somehow made his way back to the Republic. At the same time, the Imperial captain Eisek attempts to lure Shan to the Empire's service by giving him a tour of the Sun Razer, but Shan refuses Eisek's offer and he is taken to the torture chamber with Zho. However, Shan quickly frees himself and Zho, and they meet up with Teff'ith, whom Shan had ordered to remain hidden aboard their ship to avoid detection; the three then decide to destroy the Sun Razer.
Shan attempts to assassinate Darth Mekhis in order to get close to the controls for the Sun Razer's shields, but Zho sacrifices himself to save Teff'ith when they encounter Imperials as the two head back to ready their ship for departure. Despite Shan's capture, the agent outwits Mekhis and her subordinates and deactivates the Sun Razer's shields, exposing the station to the sun and thereby causing its destruction. Shan and Teff'ith escape and go their separate ways, and after reporting back to the Director and giving him data on the Sun Razer, Theron visits Satele on Tython and delivers news of Zho's death without identifying himself as her son.
In-text references to the events surrounding the Flashpoint: The Esseles place Star Wars: The Old Republic—The Lost Suns more specifically during the early stages of Star Wars: The Old Republic between the prologue and chapter 1.