Why was Commander Shepard relieved from duty?

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

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?

Solution 1:

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."