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I would assume Eric Holder plans to prosecute Loughner for the murder of Gabe Zimmerman, since he was an aide to a Democratic congresswoman. He probably doesn't care about the judge since he was a Bush appointee, but will at least go through the motions.

The federal government can prosecute the murder of a judge only if the judge was carrying out his official duties while he was killed. That may be hard to prove here, hence the delay in indicting on that count. As the article explains, this indictment is really just a placeholder until the real one can be prepared.

The state of Arizona could prosecute for murder if Holder doesn't, but if he deliberately botches the cases, then Loughner should be able to use the "no double jeopardy" clause to prevent the state from going after him.

SCOTUS has held, rightly or wrongly, that double jeopardy doesn't apply to prosecutions by the federal government and a state. So Arizona will probably indict for all of the killings, both of the federal officials and the other victims.