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1 - Arrival
With Matriarch Benezia defeated and the coordinates for the Mu Relay now in your possession, you'll call another meeting into the Normandy's comm room. Your squad will come to the conclusion that you shouldn't just rush off chasing the Mu Relay blindly, so your next destination should be Virmire to see what else you can learn about Saren.
When you dismiss the crew, Joker comes over the comm system and offers to patch you through to the Council. The Council is shocked to hear that Rachni were discovered on Noveria and will question your decision regardless of whether or not you let the Rachni Queen live or gave her an acid bath.
If you've actively been pursuing a romance with two of your squad members (Ashley and Liara or Kaidan and Liara), then they'll approach you after you're done speaking to the Council and demand that you make a decision. If you're a male Shepard and want to pursue things with Ashley or if you're a female Shepard and want to pursue things with Kaidan, then tell Liara goodbye at the end of the conversation. If you want to pursue things with the asexual Asari, then tell Ashely or Kaidan goodbye. If you try choosing the "can't I have both of you?" line, Ashley or Kaidan angrily leaves the comm room and you're left only with Liara as a choice.
2 - Galaxy Map
At this point in the game, you'll probably want to roam the galaxy and take care of any optional assignments you've acquired. You will technically have another chance to do them after finishing Virmire (your next plot-critical planet), but you won't be able to return to the Citadel afterward (for, say, a reward).
When you've finished all pending assignments or have simply decided that you'd rather proceed with the primary storyline, you should plot a course for the
Virmire: Landing Zone.
3 - Kaidan
During your sixth visit to the Normandy, Kaidan will tell you more about his training under Vyrnnus (after a bit of comforting, if you were put into the position of choosing Liara over him earlier). His story even gets a little darker when he reveals that he issued a biotic kick to Vyrnuss' face and snapped his neck while defending a fellow biotic from their teacher's wrath. After some time in recluse, though, he signed up once again to serve the Alliance.
This latest conversation with Kaidan will unlock the
Salarians: Biology codex entry.
4 - Shepard's Locker
Your locker has been restocked with new items since your last visit, so go ahead and grab them.
5 - Aid Station
Don't forget to replenish your stock of Medi-gel.
6 - Liara
Liara really doesn't have anything to say during this visit to the Normandy, though you may have to give her a bit of comforting if you were put into the position of choosing Ashley or Kaidan over her earlier.
7 - Alliance Requisition Officer
As usual, check with the Alliance Requisition Officer to see if he has any new items available. If you've acquired the Rich achievement, then the Spectre Master gear should be within your price range by now.
8 - Garrus
With three plot-critical planets behind you, Garrus is starting to get a little worried that you might never catch up with Saren. Ease his mind, then listen to his concerns that the Council might just "drag their heels" should you even bring Saren back to them anyway. Garrus believes that Saren should be killed when found just to avoid any chance of him escaping or receiving leniency from the Council.
After the both of you have stated your opinions on the situation, you'll receive the
Turians: Government codex entry.
9 - Ashley
Ashley tells you that she's taking a moment to observe Armistice Day, or the anniversary of the First Contact War. Delve into the subject a little deeper to learn that her grandfather was General Williams, "the only human ever to surrender to an alien race." She'll tell you more about the battle that he fought against the Turians and what happened to him afterward, though she seems pretty ashamed about the whole ordeal.
When the conversation has concluded, you will have unlocked the
Space Combat: Planetary Assaults codex entry.
10 - Wrex
Strike up a conversation with Wrex during this visit to learn more about his reasons for being a mercenary. After learning that Wrex thinks that "killing for credits simplifies things", you'll unlock the
Krogan: Military Doctrine codex entry.
11 - Tali
Tali doesn't have much to say at the moment, though she does take the time to thank you for treating her as an equal and not a "second class citizen" like most other people.