Prologue: Cipher Nine
The Imperial Agent lands on Hutta and makes their way to a holocommunicator, where they contact Keeper, the leader of Imperial Intelligence. The Agent is then told that they are on Hutta to try to convince Nem'ro the Hutt to join the Empire. As can be expected of an Imperial Agent, this will be accomplished through subterfuge, so the Agent is told that they need to obtain a cover identity.
The Agent is directed to an Arcona named Jheeg who has worked out a plan for the Agent to assume the identity of the "Red Blade". The real Red Blade is a famous criminal whose appearance and race is unknown. Under the guise of the Red Blade, the Agent is directed to bring gifts to Nem'ro. However, the gifts that Jeeht acquired for the Agent's use are stolen from the docks by gang members. The Agent kills the gang members and retrieves the gifts, delivering them to Nem'ro's Palace. Nem'ro is pleased with the gifts and gives the Agent permission to do business on Hutta.
While at Nem'ro's Palace, the Agent establishes a relationship with one of Nem'ro's lieutenants, Kerrals Jarvis. Keeper believes that the best way for the Agent to ingratiate themself into Nem'ro's organization and influence an alliance with the Empire is through Kerrals. The Agent learns from Kerrals that Nem'ro's operations are under threat from a rival Hutt, Fa'thara. This leads the Agent to perform a number tasks for Kerrals, undermining Fa'thara's operations.
Unfortunately, Keeper learns that Kerrals' sons have crossed paths with a Sith of the Empire, leaving one dead, and the other severely wounded. This will no longer make it possible to use Kerrals to influence Nem'ro to ally with the Empire. The Agent is directed to eliminate Kerrals.
While performing the tasks for Kerrals, the Agent catches the eye of Kaliyo Djannis, an enforcer working for Nem'ro. Following the subsequent incident with Kerrals, Kaliyo confronts the Agent. However, Kaliyo's intentions are not to expose the Agent, but rather get in on whatever action the "Red Blade" has going. The Agent and Keeper decide to reveal their intentions to Kaliyo and obtain her services.
Keeper directs the Agent and Kaliyo to forge fake evidence of an alliance between Fa'thara and the Republic. The Agent and Kaliyo infiltrate Fa'thara's Palace, seizing data records which they modify for their purposes. Based on the data records and believing his rival is allied with the Republic, Nem'ro begins to reach out to the Empire for allies of his own.
The Agent is soon given their first mission to locate and collect some valuable intelligence from an alien slave Jurithus. To locate Jurithus the Agent is directed to start by interrogating a slave leader at the The Unfinished Colossus where a slave rebellion is underway. Before heading out, the Agent meets the various support personnel including Watcher Two who becomes their primary contact with headquarters.
Shortly after obtaining the required intelligence, the Agent is summarily directed to Imperial Citadel for a private meeting with Darth Jadus. The Darth has taken an interest in the Agent and explains his intentions to forge the Agent into an effective tool for the Empire. This will start with a new priority mission.
The Keeper informs the Agent that he must assist in identifying and eliminating dissident faction on Dromund Kaas. The Agent starts by locating Samara Mindak at the Nexus Room Cantina. The Agent persuades Samara into helping gain access to her father Theovor Mindak. The Agent confronts Theovor, ultimately accessing his computer and retrieving new intelligence on the dissidents.
As a result of Watcher Two processing the new intelligence the Agent learns that the dissidents are planning to blow up the power system under Kaas City. They intend to overload long forgotten conduits at the Dark Temple causing a chain reaction into the city. Darth Jadus insists that the Agent alone thwart instead of a full assault due to the sanctity of the Dark Temple.
The Agent is successful in stopping the terrorists at the Dark Temple, but upon returning to Imperial Headquarters learns that a secondary target, the Imperial dreadnaught Dominator, was destroyed killing Darth Jadus who was aboard. The Agent is directed to quickly act to prevent a group of dissidents from fleeing by using a mouse droid to infiltrate and sabotage their ship.
After returning from this final mission on Dromund Kaas, the Agent watches, alongside the support team at headquarters, a pirate broadcast by The Eagle, the apparent leader of the dissidents. Imperial Intelligence is unable to jam the signal and the broadcast is seen throughout the Empire. The Eagle takes credit for the attack on the Dominator and promises more attacks as long as the Empire continues to be ruled by Sith leaders who continue infighting that the dissidents feel is keeping the Empire from obtaining the rise to glory and strength it was promised.
The Agent is promoted to cipher Nine and asked to lead the search to eliminate the Eagle and his organization. The Keeper explains that along with the promotion, the Agent is given a large amount of freedom to conduct the investigation, including a new Starship and ability to recruit team members. Watcher Two will continue to be their liaison back to Imperial Intelligence.
Chapter 1 (Heart of Terror)
Across the four planets of Chapter 1, Balmorra, Nar Shaddaa, Tatooine, and Alderaan, the Agent takes down four deadly terrorist cells, each supplying The Eagle's network. Along the way, the Eagle's plan of using weapons of mass destruction known only as the "The Eradicators". Further investigation reveals that these are biological orbital strike weapons that fire randomly if not issued commands. After taking down the terrorists' main financier on Alderaan with the help of Vector Hyllus, the Agent rushes back to Hutta, where spies have sighted the Eagle. Before the fight he mentions a "Patron", a traitor amongst the Empire's ranks, that has masterminded the entire plan. After the fight, Cipher Nine is praised and is informed of a Imperial Cruiser in deep space. The Agent travels to the ship with the help of Watcher Two and discovers that the Eagle's Patron is Darth Jadus. He attempts to recruit the agent to execute his plan of firing the other eradicators, but the agent has the other half of the command codes, ones acquired from the Eagle's base. This leads to a complicated decision. You can give him to codes to distract him, while you cripple the ship so the Dark Council can capture him, or not give him the codes and fight him, but Jadus will escape. Or you can side with Jadus and he will give you the task to kill his daughter, Darth Zhorrid, so that he can reassume his place in the Dark Council and reshape the Empire according to his image. If you do so, he will name you as the Hand of Jadus. It is your decision that will effect the Galaxy forever.
Chapter 2 (The Mind Trap)
With the Eradicator threat behind, Keeper is promoted to Minister of Intelligence, Watcher Two is promoted to Keeper and issues the Agent a new assignment: to infiltrate, as a double agent, the Republic SIS and learn the plans of Ardun Kothe, the Jedi spymaster. Cipher Nine joins the special forces group under the cover of an Imperial defector, and is given the codename Legate. After proving your loyalty to another operative called Hunter, you meet Ardun Kothe, who triggers a codephrase to subvert the agent's free will in case their true loyalties remain with the Empire. He wants you to continue your work inside the Empire, reporting back as a double agent. The codeword prevents Cipher Nine from reporting to Intelligence about both the brainwashing and Ardun Kothe's plans. The Agent is directed to Taris, where he must find a rogue Jedi. The Jedi is attempting to gain possession of an Ultrawave Transmitter in order to control the rakghouls of Taris. After the mission, the Agent experiences strange hallucinations, side-effects of the mind control. Watcher X of Nar Shaddaa manifests within the Agent's mind, directing them to cure themselves of the codeword. The Agent travels back to Dromund Kaas where s/he finds that the Minister of Intelligence authorized Mind Control commands on Cipher Nine. How the SIS got hold of the codes, Cipher Nine does not know. Cipher Nine finds a possible cure for the Mind Control, and goes and creates the serum for it on Quesh. While it is doing its work, the Agent travels to Hoth to find a lost Republic warship. After this, Ardun Kothe summons his team to Quesh, where he reveals his plan to steal the Shadow Arsenal; a cache of undetectable missiles that would serve as both an effective deterrent to war and a massive first-strike advantage for the Republic. The Agent foils his plan. After returning to headquarters, the Agent learns that the Empire is now at war again with the Republic. The Imperials then realize the one called “Hunter” is part of a third group manipulating the war for their own cause. The Agent is ordered to eliminate this third party.
Chapter 3 (The Hidden Masters)
Hunter was seen on a contested asteroid space station that promptly surrendered to the Empire. Upon pursuit, it is revealed that Hunter orchestrated a droid massacre of the occupants to raise tensions between the Empire and the Republic, forcing a hot war. The Agent departs for the Belsavis prison world, where Hunter was seen. The bunker the Agent needs to infiltrate is Megasecurity Ward 23, so the Agent enlists the help of four criminals to break in. Upon breaching Cipher Nine then learns the group’s name; The Star Cabal, who has manipulated wars for a thousand years. Back at headquarters, the Imperials decode a holorecording found within the bunker. It contains a mind trap, putting Keeper into a coma. Cipher Nine then goes to Voss, looking for information about a Star Cabal member, a local legend with the Voss, known as “The Shining Man” Cipher Nine finds The Shining Man’s ship along with valuable information. S/he is recalled to headquarters, where the agent learns that the Dark Council has dissolved Imperial Intelligence, a symptom of Star Cabal manipulation for fear of fully deciphering their plans. They allow the Agent's team to continue operations, with the exception of Kaliyo, whom they arrest for her criminal record. Cipher Nine and their team is transferred into the military, and stationed on Corellia's frontlines under the incompetent Darth Razer. The Agent continues looking for the Star Cabal’s base of operations. S/he is contacted by Keeper, who has recovered. Together, the Agent and Keeper find The Star Cabal’s home base. Keeper later helps the Agent infiltrate the council meeting, where they identify several members. They intercept Hunter, where they finally defeat him and procure the Black Codex. Back at an Imperial ship with the few remaining members of Intelligence and their allies, the Agent becomes nobody. Cipher Nine is removed from every database in the galaxy, and the agent becomes a silent watcher, showing himself against the Republic only when needed. The story ends with the Agent’s crew jumping to Hyperspace, thus ending the Agent’s story.
This concludes with defeating a group of people who don't use the force and want to dethrone both Jedi and Sith in the hope wars related to promoting each side of the force end. The practices and information used to keep members of this group secret can be given to Sith (who may threaten to kill the Agent if it isn't turned over but can be defeated), given to a Jedi (who may respect the Agent regardless of the choice he or she makes), the Agent's boss, and will be used by the agent his or her self to become hidden and that much more effective a spy or assassin.