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1 - Arrival
When you first arrive on the Normandy after the ship has been put in your command, Joker exchanges a few words with you about how Captain Anderson got "screwed." The staff onboard is behind you regardless of the situation, though, so Joker suggests that you use the intercome to say a few words to the crew. As with most other dialogue options, the top choices pursue a more uplifting Paragon tone while the lower choices are of a more over-the-top Renegade tone. You will gain points accordingly, so choose wisely.
After your speech has concluded, you can strike up another conversation with Joker to get a status report on the Normandy and to learn more about his personal life. You get a little more than you bargained for, as a matter of fact. Joker reveals that he has an incurable disease called Vrolik's Syndrome, or brittle bone disease, that keeps him from moving around much lest he break a couple of shin bones. As a result, he has spent a majority of his life in a pilot's chair, making him the best pilot the Alliance has to offer - or so he claims.
2 - Viewport
Take a moment to look out the viewport window to Joker's left before exploring the rest of the ship. This will unlock the FTL Drive: Appearance codex entry.
3 - Galaxy Map
Just approaching the Galaxy Map once you're in control of the Normandy unlocks the Citadel Space codex entry. Once you're ready to leave the docking bay at Citadel Station, you should use the Galaxy Map to pick your next destination. For the purposes of this walkthrough, I recommend landing on Therum (within the Knossos system of the Artemis Tau cluster) and begin your search for Dr. Liara T'Soni. You can also try some of the uncharted locations from your previously acquired assignments, though you can always move on to those later.
4 - Personnel Manual
Check the Personnel Manual on your new desk to unlock the Systems Alliance: Military Ranks codex entry.
5 - Kaidan
For the most part, all of the important conversations you have with your squad members will occur on the Normandy. If you've just docked at a major port or are ready to depart, you should check each member to see if they have anything new to say.
For future reference, this is where Kaidan will be stationed when onboard the Normandy. Unfortunately, he doesn't have much to say prior to leaving the Citadel Station for the first time.
6 - Sleeper Pod
Inspect this crew member's sleeper pod to unlock the Starships: Crew Considerations codex entry.
7 - Aid Station
As usual, the medical clinic's aid station can be used to replenish your squad's stock of Medi-gel.
8 - Doctor Chakwas
Again, for future reference, this is where you'll usually find Doctor Chakwas when navigating the Normandy's interior. Assuming you've already talked to her about Kaidan before going to the Citadel, she doesn't have anything more to say.
9 - Alliance Requisition Officer
You probably have a selection of items lying around that your squad isn't using, so make use of your personal merchant and sell them for some extra credits. If you picked up some of the manufacturer licenses back in the Citadel, then you should also browse his goods for any new additions.
10 - Garrus
For future reference, this is where Garrus will be stationed onboard the Normandy. If you want, you can talk with him about his position with C-Sec and he'll reveal some annoyances he has with the way they handle things. This conversation is mostly an introduction into his motives, though, so don't expect any journal or codex entries just yet.
11 - Ashley
For future reference, this is where Ashley will be stationed when onboard the Normandy. You can talk with her a bit about the mission on Eden Prime, but then she tells you that she needs to get her "duties squared away." Maybe next time she'll have more to say.
12 - Wrex
For future reference, this is where Wrex will be stationed when onboard the Normandy. Wrex actually has a bit to say during this visit to the Normandy, so make sure you explore all dialogue options with him. Primarily, he'll tell you about the genophage and how it's effectively destroying their entire species. This will unlock the Krogan: Genophage codex entry.
13 - Tali
For future reference, this is where Tali will be stationed when onboard the Normandy. The Quarian actually has a lot to say before making your first flight as Captain. If you quiz her about her people, the Geth, and the concept of their pilgrimages, she'll feed you a considerable amount of background information. When you're finished exploring all dialogue options, you should have unlocked the Quarians: Economy, Quarians: Government, and Quarians: Migrant Fleet codex entries.
14 - Engineer Adams
Adams is very knowledgeable when it comes to Alliance ships, having served on many of them during his career. If you ask him about the Normandy, its stealth system, and his personal life, you'll unlock the FTL Drive, Military Ship Classifications, and Normandy codex entries.
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