The Trayus Academy stood as an age-old Sith institution of learning, situated on the world of Malachor V. Revan, a Jedi Knight, stumbled upon the derelict structure during the Mandalorian Wars. During the subsequent Jedi Civil War, he exploited the academy to convert Jedi to the dark side and mold them into Sith assassins. Following the defeat of the Sith forces in that war, the Academy became the central base of operations for the Sith Triumvirate, continuing its function as a training facility for Sith assassins until Malachor V's destruction in 3951 BBY.
Millennia prior to the Mandalorian Wars, a Sith Empire erected the Trayus Academy as a training center. Eventually, the Sith abandoned both the Academy and the planet itself.
In 3961 BBY, during the Mandalorian Wars, the Jedi Knight Revan rediscovered Malachor while searching for potential bases along the Outer Rim. He had heard tales of a world forbidden to the Mandalorians by their own cultural taboos. Driven by curiosity to understand why Malachor V held such significance for the Mandalorians, Revan secretly investigated the planet, unknowingly about to unearth far more than he anticipated.
Revan located the Trayus Academy, and within its confines, he rediscovered the location of Korriban and found evidence that the Sith Empire persisted beyond known space, remaining a threat to the galaxy. Without the knowledge of even his most trusted allies, like Malak at that time, Revan established a stronghold and harnessed Malachor's dark side energies to bind his most loyal followers to his will. This led to the creation of the Sith assassin order.

Upon returning to the war, Revan guided the Republic to victory over the Mandalorians. One year after his rediscovery of the Trayus Academy, Revan orchestrated a final confrontation with the Mandalorians above Malachor V. In complete secrecy, he had prepared a superweapon, referred to as the "Mass Shadow Generator," intended as the centerpiece of a trap designed to conclusively end the Mandalorian Wars. Meetra Surik, a trusted Jedi General (who would later become the Jedi Exile), oversaw the device's deployment.
Revan baited the Mandalorians to Malachor, and as the battle intensified, he ordered Surik, one of his most trusted generals, to activate the generators. The resulting cataclysm drew a significant portion of both the Mandalorian and Republic fleets into a massive gravity vortex, crushing countless ships into the planet's crust and fracturing the world to its core. Remarkably, the Trayus Academy survived the catastrophic event without being destroyed.
Following his victory, Revan journeyed with Malak to the Unknown Regions in search of the Sith Empire. There, on Dromund Kaas, they encountered the Sith Emperor and were subjugated to his will, becoming Darth Revan and Darth Malak. The Emperor then tasked them with finding the Star Forge, intending to use it to accelerate the construction of the Sith armada. During their search, they broke free from the Sith Emperor's control and established their own Sith Empire. During the Jedi Civil War, approximately 3959–3956 BBY, Darth Revan utilized the Trayus Academy as one of several clandestine Sith bases dedicated to converting captured Jedi. Throughout the war, his Sith assassins and other specially trained forces captured Jedi and brought them to the Academy. The location's corrupting influence weakened their resolve, making it easier for Revan and his loyal followers to sway them to the dark side. In these locations, he transformed numerous Jedi into devoted Dark Jedi and Sith assassins for his empire.
One year after the Galactic Republic defeated the Sith during the Jedi Civil War, a redeemed Revan embarked on a solitary quest to the Unknown Regions to confront the Sith Empire. Meanwhile, Kreia, Revan's former Jedi Master, suspected that her teachings had inadvertently led Revan to the dark side and began searching for her former pupil—a search that ultimately led her to Malachor V. Upon setting foot on the planet, Kreia was overwhelmed. She succumbed to the dark side, becoming Darth Traya. She studied the planet's secrets and assumed command of the Trayus Academy and the Sith Assassins who remained there. Traya reestablished the Academy to train, convert, and create a new generation of Sith, who were then deployed to destroy the Jedi Order.

Darth Traya soon discovered two Sith Lords in whom she saw the potential for the death of the Force. Darth Nihilus and Darth Sion aligned with her cause, and together they established a Sith Triumvirate. Operating from their hidden Academy on Malachor V, the Sith Triumvirate commanded legions of Assassins who hunted the remaining Jedi to the brink of extinction. Darth Traya successfully united the fragmented Sith forces through their shared hatred, leading them to victory once again, but her triumph would not save her. In a sudden act of betrayal, her two apprentices joined forces, stripped her of her power, and banished her.
In 3951 BBY, Kreia located Meetra Surik, the only Jedi who had fought alongside Revan against the Mandalorians at Malachor V and remained uncorrupted. Driven by a desire to rid the galaxy of her fallen apprentices and ultimately bring about the death of the Force, Kreia orchestrated events to create a final confrontation between herself and Surik at the Trayus Academy. After defeating Darth Nihilus, Surik arrived at the Academy to confront the Sith lurking within. She invaded the academy and eliminated every Sith minion in her path. Shortly after defeating Darth Sion and killing Kreia in a series of lightsaber duels, Malachor V was torn apart when the Mass Shadow Generator was reactivated on Surik's orders.
From the Malachor Depths, the entrance to the Trayus Academy opened into an antechamber, which then connected to the complex's eastern and western halls. The Trayus Crescent, situated to the west, was a hall featuring numerous alcoves frequently occupied by Sith commandos. To the east, the Trayus Proving Grounds consisted of a maze of small, cramped rooms where many Dark Jedi and Sith commandos could be found. Both wings converged at the Academy's central area, the final open space before reaching the innermost sanctum of the Trayus Academy, known as the Trayus Core.
In the video game Star Wars: Knights of the Old Republic II: The Sith Lords, if the player chooses the dark side path, under this non-canonical timeline, both Malachor V and the Academy would remain intact.
It remains unknown whether the Sith Empire founded by Adas or the Sith Empire ruled by the Exiles and their descendants constructed the Trayus Academy, or when it was abandoned.