The first time you have access to the Citadel, you can find Kelly Chambers at the Docks: Holding Area providing she survived the Suicide Mission in Mass Effect 2.
Choice: Identity or Refugees
When you first converse with her, you’ll have a choice to make at the end of the conversation which determines her fate. These choices are “Take care of the refugees” or “Change your identity”.
Choice: Take care of the refugees
By choosing “Take care of the refugees” you’ll be signing her death warrant because, when you visit the Citadel again after the Mission Priority: Citadel II, you’ll find out that she was gunned down by Cerberus soldiers who was asking for her. This will be the end of Kelly, and the end of your Romance with her.
Choice: Change your identity
By choosing “Change your identity”, when you visit the Citadel again after the Mission Priority: Citadel II, you’ll be able to converse with her again, and you’ll find out that, by you telling her to change her name, saved her life. You’ll also be able to continue your Romance with her, if you chose her in Mass Effect 2.
Providing Kelly survives your first conversation with her, the third time you converse with her, she’ll confess to you that she was sending reports about you to the Illusive Man whilst you were working for him. This choice can also affect her fate.
Choice “It’s okay” or “You did what?”
After she confesses to you about the reports, you’ll be able to respond in one of two ways, these choices will be: “It’s okay” or “You did what?”.
Choice “It’s okay”
If you tell Kelly that “It’s okay”, you’ll tell her you understand why she did, what she did. This will make her feel like a huge weight is lifted from her shoulders, and she’ll thank you for your understanding. This will reward you, with her as a War Asset for 10 Military Strength.
Choice “You did what?”
By telling Kelly “You did what?”, you’ll scold her, sending her to tears. The next time you go to the Docks: Holding Area, Kelly is nowhere to be found. If you used your Spectre terminal to order the release of Gabriella Daniels and Kenneth Donnelly, they’ll be back in engineering on the Normandy, and you’ll overhear them talking about Kelly, saying she committed suicide with a cyanide pill.