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.
Arriving at Nar Shaddaa, the Consular is told they have to find Duras Fain, one of the corrupted Jedi Masters, who lead a cult called the Guiding Hand, which is causing difficulties for the Hutt Cartel and risks the Hutts joining the Empire. On the planet, the Consular needed to locate an Exo-technology expert, Tharan Cedrax, but arrived to only find his holo sentient assistant, Holiday, who told them he's not arrived yet. They find Tharan and he helps the Jedi infiltrate the gang. The Consular meets Fain via holo, who discovered the Jedi Consular's true intentions. With Tharan and Holiday's help, the Consular tracks Fain to Shadow Town. The Consular returns to Tharan, and after fending off a Hutt Cartel representative, the Consular receives a device to make them immune to Fain's mind control. They find Fain who talks about Malachor Three and how it cost the life of Parkanas Tark. He tries to control them, but the tech successfully prevents it. Defeated, Fain mentions Vivicar and they deal with the Hutt Cartel about Fain's fate. Arriving back to the ship, the Consular meets with Tharan who offers his services to the Consular and he and Holiday join the Consular's team.
On the ship, Syo reports of a distressed ship that has reported a crazy Jedi, Laranna Fain linked with the plague. Arriving to help, the crew of the ship mention that Laranna was hurt during an Imperial attack and when she was healed, she went crazy. They find out the man that healed her was Lord Vivicar, who infected her with the plague when he was healing her. The Consular defeats her and retakes the ship. The ship receives a message and the Consular meets Vivicar. On their ship, the Consular is informed of two more missing Jedi who were infected on the planets, Tatoonie and Alderaan.
The Consular was sent to locate Jedi Master Eriz Vossan, who was sent to study the cultures on Tatooine. The Jedi finds Vossan's guide Rowan Delk. The Consular was directed to a group of Jawas who were forced to dismantle sand crawlers for weapons by Vossan, and left a message behind for Rowan. The message helped the Jedi find out that Vossan went to the Sand People, and used them to attack the Republic and making them stronger. They find Vossan who believed that using the Sand People to destroy the weak and use them to fend off the darkness. The Consular defeats him and he mentions Parkanas and Vivicar.
On Alderaan, the Consular was set with looking for an infected Jedi Master named Sidonie Garen. She was sent to be a representative of House Organa at the Alderaan peace talks. The Consular tried to reach her, but she dodged their calls and to gain access to the peace talks, the Consular had to become a representative of one of the noble houses. Following Hallem and Lew Organa's advice, the Consular approaches allied House Teral to ask to represent them. The Consular protected the Teral family from attacks, making them look strong enough to create a proper marriage alliance with Organa. However, Lew Organa was kidnapped by House Rist. During the rescue, they find in House Rist a holo line connected to Sidonie, who orchestrated the kidnapping. Thanks to the rescue, Teral agreed to make the Consular their delegate and they made their way to the peace summit. At the summit, Sidonie was already fanning the flames of war, exposing secrets of each noble house so there could be no peace, thinking war will stop the coming darkness. The Consular stopped her and was able get the delegate to cooperate.
Once the last master's saved, the Consular realized the connection with all the infected, that Parkanas must be Vivicar. Yuon Par admits to the events and she creates a connection to Vivicar to locate him. The Consular heads to the location and finds Vivicar, defeating him and ending the plague and they are named Barsen'thor.
Chapter 2 (The Rift Alliance)
Following the success of defeating the plague, the Consular meets with the Jedi Council and the Chancellor. With war on the horizon, the planets were breaking off from the Republic. The planets formed a group known as the Rift Alliance. The Consular is assigned to be the representative of the Rift Alliance, to solve their problems, and the Consular is made a Jedi Master. The Jedi goes to the Rift Alliance ship, the Fortitude, but they are contacted by a passenger named Nadia Grell, who told them the ship was under attack by the Empire. They kill the Sith and save Nadia and the Rift Alliance ambassadors: Senator Grell, Alauni, Tai Cordan, Blaesus, Shuuru, and Diab Buin. They become passengers on the Jedi's ship and the first step in establishing relations is freeing Tai's homeworld, Balmorra, from Imperial control.
Upon arriving, Tai Cordan says that with the president captured, he's the next leader in succession. Tai said they should work with a Balmorran revolutionary called Zenith. Zenith is reluctant to work with the Republic and demands help. The Jedi helps Zenith and he joins the mission. Knowing Balmorran corporations carry a lot of political pull, Tai gathers his contacts, and the Consular recruits an important official to the cause, who provided resources for them. After securing the coporations, the next plan's to save the president from the Sith, Darth Lachris, to transfer power over to Tai. They rescue prisoners from Lachris and a prisoner tells them the location of the president. Zenith and the Jedi infiltrate the arms factory and find Darth Lachris and the president, who's frozen in carbonite. Lachris is killed but the president was severely psychologically damaged. However, Tai is made president and Balmorra joined the Republic, and Zenith is made as a liason between Balmorra and the Rift Alliance and Zenith joins the Consular. Before the leave, however, Nadia and her father reveal that someone on board had planted an Imperial monitoring device on the Consular's ship. They also say a Rift Alliance research facility was attacked on Quesh and in need of rescuing.
The Consular and their companion and Nadia go to Quesh to find the facility attacked by Sith and Imperials. While protecting the scientists, Nadia was revealed to be able to use the Force. Back on the ship, Senator Grell talks about Nadia's abilities before mentioning that the Rift Alliance needs help on Hoth.
A splinter group of the White Maw has been attacking the Rift Alliance shipping lanes to their worlds, and soldiers the Alliance sent have constantly suffered defeat. They send the Consular to join the coalition force and defeat these pirates. At the Republic Base, the Consular meets the coalition leader Lieutenant Felix Iresso, who is trying to keep order after constant defeats by a pirate, Captain Valon, who inexplicably is incapable of dying. The Jedi finds Valon, and kills him, but after returning to the base, they get a message from Valon, still alive, planning to cut off Republic heating. The Jedi is ambushed by Imperials and learns that Valon stole special armor from Imperials which gives him healing abilities that give him his invincible traits.With Feliz and his soldiers' help, the Consular infiltrates an Imperial lab to learn more about the armor, and its weakness. The Republic prevents Valon from taking a dreadnaught as a flagship and the Jedi defeats the pirate, breaking the armor. As a reward for his work, Irreso is assigned to the Consular. After the meeting, Nadia and Senator Grell said that someone on board the ship was sending messages to Valon during the mission. They suspect Blaesus, who was currently sent to meet with the king and queen of Sarkhai.
The Jedi arrives at the way station which was occupied by Imperials. They find Blaesus with Lord Kyrus. It is also revealed that Blaesus, himself, is a special Sith, called a Child of the Emperor. He explains that thanks to the First Son, he and other Children of the Emperor could be shielded from the Jedi sensing abilities, allowing them to infiltrate various areas of the Republic without risk of exposure. The Consular kills Kyrus and Blaesus, saving the royal family. The Jedi is informed that war has broken out, and the Children are becoming active, sabotaging the Republic. The Consular's charged with finding more allies to aid the Republic. The Cosular heads to Tython to hear the wisdom of the Noetikons.
Chapter 3 (The Children of the Emperor)
The Consular uses the Noetikons, who advise the Jedi of an army imprisoned years ago on an unknown planet, which could be used to defend the Republic. The Consular follows the clues to Hoth, where they found a recording, restating the imprisonment of Esh-kha, a warring race who tried to wipe out life in the galaxy. It also spoke of a faction group of Esh-kha who did not agree with the genocide, but were imprisoned with the rest of their race, and the hologram gave to coordinates of the prison planet, Belsavis.
Assistant Komi directed the Consular to the Commander Geland, who would know more abut the vaults of the prison. Following to Geland's last known location, they find Geland's team dead, with Geland missing. Komi arrives and destroys the cameras and tells the Consular that Geland killed his team with Force abilities, revealing himself to be one of the Children of the Emperor. While searching for the Esh-kha, Geland sends the prison defenses on the Consular and the Jedi is contacted by a mysterious person. This person guides them to the rebel Esh-kha who were lead by their leader, "Hallow Voice". The anonymous guide is revealed to be a Rakata named Lhunu, who wished to fix the mistake in imprisoning Hallow Voice and his followers. The Consular frees Hallow Voice's followers before making their way to Hallow Voice himself. They arrive to Hallow Voice's prison to find Geland who tried to kill Hallow Voice. The Jedi kills the Child of the Emperor and saves Hallow Voice, and he adds his forces to the Republics.
Arriving on the ship to introduce their new ally, Nadia tells them her father was kidnapped. They track down the kidnapper and Nadia and the Consular find the Senator dead and Nadia kills the kidnapper. Her father's last will asked that Nadia be taught by the Barsen'thor, which was accepted and Nadia became the Consular's padawan. The alliance needed more allies and suggested Voss as the next destination to find them.
The Consular talks to Sophia Farash to help recruit Mystics in fighting the Empire. She suggests instead of recruiting someone already a Mystic, they help a potential, Gaden-Ko complete their trials to become a Mystic. The Consular finds Gaden-Ko in a cave, where his family had been killed protecting him. On the pilgrimage, Gaden-Ko is critically wounded by an Imperial and needed to be healed. After Gaden-ko is fixed at the Shine of Healing, he tries to receive a vision but he and the Consular are needed to help commandos against Gormak. They go to the Deep Cradle in the Nightmare Lands after rescuing Republic forces. Gaden-Ko has a vision as the Jedi protects him, and Gaden-Ko becomes a Mystic. Upon returning to Voss-Ka, and it is decided that Gaden-Ko should travel with the Consular, along with his entourage of commandos and healers. However, in the space station, Sophia Farash meets up with them, and she reveals herself to be a Child of the Emperor and tries to stop them from leaving. Upon her defeat, she reveals that the First Son does not know his own identity, or his nature as a servant of the Emperor until he's active, and she's taken into Voss custody.
Arriving on the ship, Master Syo calls a war council. A fleet heading toward Corllia has a valuable flagship, the Javelin, the the Consular is tasked with capturing. After taking the bridge, the Jedi finds out the ship was ridged with explosives, as a trap. While disabling as many explosives as they can, the crew escapes the ship, though one companion was forced to take the Javelin's escape pod, which landed on Corellia.
Tai Cordan speaks wih the Consular about Corellia and that the escape pod the companion used to escape the Javelin landed in one of the ship yards. Cordan said Master Syo completed the work on the Guardian Holds, vital building in the city that would be used in winning the city, which are now outfitted with special defenses. With help from the Republic, the Consular located their missing companion, who gained vital information of the First Son from the Javelin. They view the footage, where it's revealed that the First Son is none other than Master Syo. Contacting Syo, the First Son took control of the Jedi Master and the Guardian Holds were invaded and secured for the Empire by the Children of the Emperor, who infiltrated them prior. The Consular and the forces of the Rift Alliance retook some Guardian Holds, killing Children of the Emperor in the process. The Consular reaches Guardian Hold One where one of the officials is a Child of the Emperor. The survivor tells the Consular the First Son is hiding beneath the city and tells them the entrance of the cavern.
The Consular enters the underground, where they find the First Son. The Jedi battles and defeats the First Son for good. His defeat removed the shielding of the other Children, allowing the Jedi to detect and defeat them. The Consular returns to Coruscant, who rewards them and the Rift Alliance.