The Imperial Agent lands on hutta and makes his/her way to a holocomunacator where he/she contacts keeper, the leader of imperial intelligence, the agent is then told that he/she are on hutta to try to convince nem'ro the hutt to join the empire, the agent is also told that he/she will have a cover identity and is then directed to a alien named jeeht who will give you a cover identity.the agent meets with jeeht and is told that his cover identity is that of the "red blade", a famous criminal who's appearance and race is unknown, the agent is also to bring gifts to nem'ro but is told that the gifts wher stolen from the docks by gang members and you will have to retrieve the gifts, you then continue to kill the gang members and take the gifts to nem'ro's palace where you meet nem'ro's lieutenant kerrals javis, Nem'ro is pleased with the gifts and gives you permission to do business on hutta. Working undercover, you forge fake evidence against Fa'thara, a rival hutt, showing him working with Republic forces. Seeing this, Nem'ro promices to join the Imperials. Mission Complete! You are then directed to Dromund Kaas, where you have to foil an terrorist attack. Along the way, you meet a Sith, Darth Jadus, who makes you his "chosen agent" Later, you rush to the Dark Temple, where terrorists are trying to take out Kaas City's power. You succeed, but upon returning to headquarters, you learn that a transport in space has exploded, killing Darth Jadus. Headquarters then get a holorecording from someone calling himself "The Eagle". He promises to destroy the Empire. Thanks to your actions at the Dark Temple, you are promoted to the rank of Cipher Nine, and are givin a ship to use. You are instructed to hunt down the terrorists.
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 a final cell on Alderaan, 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 dicision. 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. It is your dicision that will effect the Galaxy forever.
You have foiled Jadus's plot to destroy the Empire, either way, and 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 Leget. 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 you 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. 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 known. 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, Ardun Kothe summons his team to Quesh, where he reveals his plan; to steal the Shadow Arsenal; a cache of super undetectable missiles, 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.