User blog comment:James12708/Why Exactly is Sheperd on Earth if Arrival Wasn't Completed/@comment-4967682-20121202110330/@comment-2228120-20121202183430

If I recall correctly, Shepard is reinstated as a Spectre but at the same time, he is recommended to keep a low profile. And the Alliance is not totally cool with him, either - Anderson isn't telling him everything, and there is a request for his arrest which Hackett turns down, so it's rather that Shepard is allowed to operate freely as long as he is useful and his friends can keep the Alliance off his tail. Once he turns himself in, that protection is insufficient.