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The Jedi Consular, still a Padawan, lands on Tython where they meet their new master Yuon Par. They immediately learn that Flesh Raiders are attacking the grounds of the Jedi Temple. Normal training is cast aside as the padawan is directed to assist by retrieving four ancient holoprojectors that the Jedi founders created and which are located on the template grounds. After watching and retrieving the first three holoprojectors, the padawan discovers that the fourth holoprojector is missing. Upon returning to Master Yuon to discuss the missing holoprojector, the padawan meets Qyzen Fess a Trandoshan and unlikely friend of Master Yuon. Qyzen is on Tython hunting and collecting points in the eyes of the Scorekeeper, a key aspect to the Trandoshan lifestyle or religion.
The padawan learns that the missing holoprojector was created by Rajivari, a founding Jedi who had succombed to the Dark side of the Force. Master Yuon suggests that the padawan inquire about the holoprojector at a nearby Twi'lek village. Kalikori Village was established on Tython without consent of the Jedi by Twi'leks fleeing persecution. The captain of the village defenses reveals that Nalen Raloch, a Twi'lek dueling champion and village protector, took the holoprojector.
Nalen, being force sensitive, has fallen under the influence of the dark side of the force through the teachings of Rajivari. He hopes to use his newly acquired force abilities to eradicate the Flesh Raiders and protect the Twi'lek village. Rajivari's holoprojector contains clues to greater power through the legendary Fount of Rajivari. The padawan is directed to pursue the clues and stop Nalen. Along the way, the padawan saves Qyzen Fess, after the Trandoshan is captured by Nalen. This is psychologically devastating to Qyzen, who declares all his Scorekeeper points forfeit in disgrace. The padawan convinces Qyzen to start collecting points anew as his companion as he pursues Nalen. The padawan also learns that Nalen intends to destroy the Jedi Order, a task that Rajivari attempted unsuccessfully, by destroying the Light Forge where the Jedi create their Lightsaber.
Ultimately, the padawan reaches the Forge ahead of Nalen and crafts their first lightsaber. Upon exiting the forge, the padawan is confronted by Nalen. The padawan defeats Nalen and impresses Qyzen greatly. Qyzen declares the padawan the Scorekeeper's Herald and swears his loyalty. When the padawan returns to the temple, they are greeted by Grand Master Satele Shan who gives congratulations and recognizes them as a full Jedi.
Unfortunately, Master Yuon soon collapses due to a mysterious ailment. The new Jedi is directed to proceed to Coruscant where Master Yuon will receive medical care as the Jedi searches for a cure. Qyzen Fess, having sworn loyalty to the Jedi, accompanies him.
When the consular arrives on Coruscant he makes his way to the senate tower to check on Yuon Par. In her room, he finds her raving about "the man in the shadows" and someone called Parkanas. Yuon's doctor comes in and tells the consular that he thinks a trio of jedi holocrons called noetikons may hold a cure for Yuon's illness. This leads the consular across Coruscant in search of the noetikons. After finding them and talking with the jedi personalities imprinted within, the consular learns that Yuon's illness is in fact an ancient force plague created by a dead sith named Terrak Morrage. With it, Morrage killed thousands of jedi until a jedi healer developed a shielding technique that cut off infected jedi from Morrage's power. Each time the healer used this technique, however, some of his strength was consumed. He was able to heal hundreds of jedi, cutting them off from Morrage one by one, until his strength was depleted completely and he died. Morrage was killed, however, and the plague was stopped. The noetikons inform the consular that if they can be reconnected to the archives within the jedi temple ruins they will be able to teach the consular the shielding technique, though it would come at the expense of his own strength. The consular agrees and takes the noetikons to an archives terminal in the jedi temple, activates them, and learns the shielding technique. A sith and two followers enter the chamber and confront the consular. The sith destroys the noetikons and attacks the consular. The consular defeats the sith then returns to the senate tower where he performs the shielding ritual on Yuon Par. The ritual is a success and Yuon is freed from the Plaguemaster. The jedi council summons the consular to the council chamber and informs him that this may not have been an isolated case. Jedi masters around the galaxy are no longer able to be contacted. The council asks the consular to seek out and shield these masters. The consular accepts this task and is given a ship and told to seek out two jedi masters on the planets Taris and Nar Shaddaa.
Chapter 1 (The Dark Plague)
The consular arrives on Taris where he begins his search for Master Cin Tykan. The consular meets with Captain Nelax and Padawan Aris who worked with Tykan. They say Tykan left with a research expedition. They contact the expidition and discover that the team needs help. The Consular rescues the team, and they say Tykan was the one who tried to kill them. They say Tykan is heading to the Junction. The Jedi arrives and finds Tykan talking jibberish, including mentioning Parkanas and a coming darkness that he must stop by destroying the Junction, and he destroys the gasline. Saving the workers, the Jedi contacts the base, discovering it's under attack by Tykan. The Jedi arrives to find it infested with rakghouls, and the Jedi closes the tunnels which gave them access to the base. Tykan apparently attacked the base and kidnapped his padawan. After saving the base, they find out that Tykan plans to destroy a reactor, which will allow pollution into the ecosystem and kill eveything. The Consular arrives and finds Tykan, who mentions a Lord Vivicar. The Jedi stops Tykan and saves the planet before returning to the ship to update Sylo of the events.
Chapter 2 (The Rift Alliance)
Chapter 3 (The Children of the Emperor)