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In the opening prologue, when the Reapers are first invading Earth, Captain Anderson and Shepard are talking. Anderson has the following line:

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What is Anderson referring to? Last thing I remember was saving the galaxy... twice, so I'm not quite sure why Shepard would get kicked out of the Alliance military.

What gives?

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The edit is so small I can't even make it...but you've misspelled the Commander's name here, every time you've used it. :) –  Shinrai Mar 6 '12 at 5:21
    
@Shinrai Thanks. Silly homophones. –  Raven Dreamer Mar 6 '12 at 5:27
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1 Answer

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This would most likely stem from two things, from Mass Effect 2:

  • Shepard's assumed association with Cerberus, a group who has its hands in many less-than-respectable activities.
  • Shepard's assumed liability in the deaths of 300,000 Batarian civilians at the end of the Arrival DLC, which threatened to give the Batarians an excuse to wage war against humanity and weaken support for the human race from the other Council races.

    This outcome is hinted at in the dialogue with Admiral Hackett at the end of the Arrival mission, in which he reminds Shepard that [he/she] would be a convenient scapegoat to avoid war and that "when Earth calls, [he/she] be there with [his/her] dress blues on, ready to take the hit."

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It can't be due to the Arrival DLC - if you've completed that, it's explicitly mentioned as such. –  Raven Dreamer Mar 6 '12 at 5:31
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Shepard's participation in destroying the Mass Relay is the canon reason for his being relieved from duty, however, as indicated by the Conviction comic. It's really the strongest thing Shepard has going against him, so it would be odd if that line weren't at least a partial reference to those events. Where was the Arrival DLC mentioned, by the way? I've completed it, but there wasn't any reference to it directly in the opening exchanges for me (perhaps I haven't gotten to it yet). –  Tim Stone Mar 6 '12 at 19:14
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Anderson has two possible lines, either "The shit you've done?" or "300,000 Batarians are dead because of you". –  Raven Dreamer Mar 6 '12 at 20:11
    
I think the default answer is just supposed to be "Cereberus". –  Raven Dreamer Mar 7 '12 at 0:52
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Some later conversation has hinted at that being a larger factor than I originally anticipated, definitely. I'm curious now whether Anderson's line is also contingent on whether or not you were complacent in the deaths of the Batarians, since in my case I know my imported save had attempted to warn them in Arrival, and I got the first line. Possible it just goofed, though. –  Tim Stone Mar 7 '12 at 1:24
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