You will receive an email from Agent Bau asking you to meet him on the Citadel.
Note: This mission must be completed before completing Priority: Tuchanka as it will be the last opportunity for the player to visit the Citadel before Priority: The Citadel II, after which it will no longer be available.
You can talk to him about what is going on and he gives you an overview. Apparently, the Alliance raided a batarian science lab where the batarians were studying Reaper tech. It turned into a massacre and the Alliance got away with nothing. However, hanar operatives were there as well and Bau believes they were indoctrinated at that time. You can ask where Bau got the information, and he said it was a "gift" from an anonymous donor. If she survived, Bau said it came from a master thief that he has been tracking, Kasumi Goto. Bau believes the gesture is genuine as she seems to want to help and compliments her on her abilities being almost salarian in nature.
They are now members of the hanar diplomatic delegation. Bau says that he has tracked several suspicious transmissions between Kahje and the Citadel. Shepard offers to look up inside the Spectre office. Bau says that he will appreciate that and as he leaves, he tells Shepard that not everyone ignored the Commander's warnings about the Reapers, and he hopes it isn't too late.
Shepard will then enter the offices, and if Kasumi Goto survived the suicide mission, and she still has Keiji Okuda's Graybox, she will decloak upon Shepard entering and offers to reveal the box's contents, as it will make little difference now. Shepard accepts. If Kasumi survived, but the graybox was destroyed, she will say she remembered enough details to piece clues together.
Head over to the "Spectre Terminal" and select the "Hanar Embassy Tracking" option. Exit the terminal and Bau says that he is now tracking the transmissions and asks Shepard to assist. Kasumi will say that hanar are predictable and that any anomalies will stand out. She also compliments Bau on his plan and how he is a good Spectre. She continues by saying that the galaxy needs more like him. Shepard then asks that since he's trying to arrest her, if it will change her opinion. Kasumi just responds by saying "Well, nobody's perfect".
Head out to the Embassy Lounge and on the other side from the stairs is a terminal. Shepard contacts Bau and comments about some strange transfers from Bolohn and Oloon. Bau will comment that Bolohn is clean as that is for his mistress, but will check on Oloon. Kasumi then cuts in by saying how odd it is that a hanar has a mistress. If Kasumi is not present, Shepard will instead comment on the oddity of a hanar with a mistress. This will prompt Bau to explain that Bolohn was pressured by his government to take up the mistress (who is asari) to help further relations between their peoples. He (Bau) also comments that if the scandal were ever reported, Bolohn would wind up in serious trouble with his government. The irony does not escape Shepard. Assuming Kasumi is present, after the comment about strangeness, she will comment back and forth with Shepard. Shepard offers to provide her with immunity should Bau ever succeed in catching up with her. She counters the offer with the extrapolation "What? So you can rope me into another suicide mission?" Shepard insists that he/she wasn't going to ask. At this point Kasumi responds with "No, but you were working your way around to it."
Head to the Docks Holding Area and access the terminal right outside the elevator. Shepard once again contacts Bau and says that Oloon is doing some heavy lifting to support the war effort. Bau says that it is clear that he isn't indoctrinated, and asks who's opposing him. Shepard says an unnamed hanar recently arrived from Kahje. Head to the opposite side of the docking bays to continue.
Access the terminal on the far end of the Docks Holding Area to contact Bau and Shepard forwards him a list of new hanar arrivals. Bau makes a comment that the list is useless as it is all face names, while the ones from the Alliance raid are soul names. Bau says that soul names aren't public and asks Shepard to tap back into their communications. Kasumi will then ask about the rest of the team and then ask about Jacob. Head back to the terminal at the elevator.
Accessing the terminal has Shepard contact Bau again and forward him the hanar communications. Bau says he's got it, a recent arrival named Zymandis. He was with the Alliance team that massacred the batarians and has been in a "special research assignment" ever since. Head back to the Embassies to continue.
Once back at the Embassies, head to the office suite on the left side of the elevator where Bau will meet you. Select Bau to continue.
Bau, Shepard, and Kasumi head into the office and Zymandis says that he has been apprehended but says that confinement is irrelevant as the work of the Enkindlers cannot be stopped. You can press him for answers as to why he is doing, and he says that the Protheans became the Collectors, because he is a loyal follower of the Enkindlers, and since the Collectors serve the Reapers, they must serve the Reapers. (If Kasumi is present for this exchange she will whisper to Shepard "You know, I support religious freedom for all species, but that's just crazy!") Shepard replies by saying that he is "a big stupid jellyfish". Then you can choose your actions, but either way, Zymandis says that the defenses for the hanar homeworld are largely automated, and can be shut down by a single virus, which he just uploaded.
Bau quickly springs into action and attempts to stop the upload, but a human standing at the door quickly puts his hands around Bau's throat. Bau attempts to throw him off, and Kasumi runs to the terminal to stop the upload. Shepard knocks out the man holding Bau and Kasumi manages to stop the upload, while Bau pulls out his gun and shoots the hanar. She then notices that the hanar has rigged a failsafe and the console explodes and knocks Kasumi against a wall, who activates her cloak. Bau says that she was there the entire time and that he intended to arrest her. Shepard says that she just gave her life for the hanar homeworld and that she was a friend. Bau takes the point and says that he intends to return the favor, with a few friends.
If the player did Kasumi's loyalty quest, after Bau leaves, Shepard tells Kasumi that she can come out now, to which she asks how Shepard knew that she was there. Shepard simply says that it was a lucky guess. Shepard then talks to Kasumi about the ongoing situation and Kasumi says that Shepard won't recruit her into a galactic war. Shepard says that the Crucible project needs experienced technical experts, and while Kasumi initially objects by saying that she isn't a scientist, Shepard reminds her that she is a thief and that the project needs resources, then tactfully reminds her of all the expensive tech that will be around and that no one will probably check her pockets at the end of the project. Kasumi agrees to that proposal as Shepard says the nicest things.
If the player did not have Kasumi in Mass Effect 2 or she did not survive the suicide mission, or if the player is starting a fresh Mass Effect 3 game, Shepard will have no interaction with her during this quest. During the final scene with Bau and Zymandis, you must choose between saving Bau (using a Renegade interrupt) or stopping the upload. Saving Bau grants you the Spectre Unit War Asset, while stopping the upload grants you the Hanar and Drell Forces War Asset. Since the Spectre Unit has a Military Strength of 40, while the Hanar and Drell Forces have a Military Strength of 50 which can be further upgraded to 58 if the player completes Citadel: Alien Medi-Gel Formula, players hoping to maximize War Assets without Kasumi around to enable them to save both assets are advised to save the Hanar and Drell Forces.
Many players across multiple platforms are finding that they are unable to interact with certain terminals at all, the second terminal being the most common issue. It is unclear exactly what causes the bug although one possible cause is leaving the Citadel after the first terminal but before the second terminal. To resolve the issue, reload to previous save game prior to starting the mission. After reloading, focus solely on completing the mission before attempting any other missions.
There is a fix for the PC version to the above problem where you can't use some terminals. http://www.youtube.com/watch?v=Vt7RKxImfT8
Another possible cause is the activation of Tracking from the Spectre Terminal. Once this is activated, many players cannot activate subsequent terminals. To resolve this, simply go to the terminal in Embassy Lobby, and never activate the Spectre Terminal (even before the mission), it isn't necessary to complete the mission; and bugs the mission often.