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 a 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 dreadnaughtDominator, 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 Cypher 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 liason back to Imperial Intelligence.
Across the four planets of Chapter 1, Balmorra, Nar Shaddaa, Tatooine, and Alderaan, you take down four deadly terrorist cells, each supplying The Eagle's network. Along the way, you are informed of by the cell leaders of something The Eagle is planning; only refrered to as "The Eradicators". You learn that these are biological orbital strike weapons that fire randomly if not commanded. After taking down the terrorists' main financier on Alderaan with the help of Vector Hyllus, you rush back to Hutta, where spies have sighted the Eagle. You find him, but before the fight he mentions a "Patron", inside the Empire's ranks, that has masterminded the entire plan. You kill him. After the fight, you are praised and are informed of a long Imperial Cruiser in deep space. Realizing this is the location of the Eagle's patron, you go there, and discover... (Major spoilers ahead) DARTH JADUS! He has manipulated all the events, and is about to fire the Eradicators. But you have the other half of the command codes, ones you acquired from the Eagle's base. He offers you to join him. 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.
With the Eradicator threat behind, you now have a new assignment. You now have to infiltrate, as a double agent, the Republic SIS and learn the attack plans of Ardun Kothe, an ex-jedi. You join the special forces group as an Imperial defector, and are given the codename Legate. After proving your loyalty, to another operative called Hunter, you meet Ardun Kothe, and he subjects you to a strange form of Mind Control. He wants you to continue your work inside the Empire, reporting back as a double agent. You cannot tell your friends at Intelligence about the Mind Control, or what the SIS is doing. The Agent is directed to Taris, where he must find a rouge Jedi. The Jedi is attempting to gain apossession of an Ultrawave Transmitter in order to control rakghouls of Taris. After the mission, the Agent travels back to Dromund Kaas where s/he find 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. 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 super undetectable missiles with which he hope to destroy Kaas City. The Agent foils his plan and kills Ardun Kothe. 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.
The agent departs for Belsavis, where Hunter was seen. The bunker the Agent needs to get to is in the Megasecurity ward, so the Agent enlists the help of four criminals to break in. Cipher Nine then learns the group’s name; The Star Cabal, which 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 due to Keeper’s condition. They arrest your companion, Kalyio. Cipher Nine is transferred into the military, and stationed on Corellia. The ex-cipher nine works alone on Corellia, looking for the Star Cabal’s base of operations. S/he is contacted by Keeper, who has recovered. Together, you and Keeper find The Star Cabal’s home base. Keeper later helps you infiltrate the council meeting, where you identify several members. You intercept Hunter, where you finally defeat him. Back at an Imperial ship with the few remaining members of Intelligence, 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.