User blog comment:James12708/Why Exactly is Sheperd on Earth if Arrival Wasn't Completed/@comment-4967682-20121202110330/@comment-2228120-20121202200310

Because he handed himself over on a silver platter. And the Council and the Alliance are two separate entities, each with its own agenda. For the Council, Shepard is a Spectre operating outside the law (or perhaps not, but it is their choice if they decide to overlook his activites; either way, there is no telling what they would have done, had he given up to them and not the Alliance). For the Alliance, he is still Commander Shepard, and as such subject to their jurisdiction.