A local law blogger says (emphasis in quoted material and original source):
Judge Cooke explained that because "in Counts I, II, and III, the government alleged one and only one conspiracy, with one and only one purpose and object for each of the conspiracy counts," Count I is multiplicitous and must be dismissed. . . . Count I -- conspiracy to murder, kidnap, and maim persons in a foreign county, in violation of 18 U.S.C. 956(a)(1) -- is by far the most serious count, carrying a life maximum. Counts II and III carry far less serious maximum penalties . . . . An appeal will delay indefinitely the current trial setting in January, so Mr. Padilla will have to spend more time in solitary confinement. . . . In addition to dismissing Count I, Judge Cooke also found that Count II was duplicitious. A charge is duplicitous if it alleges two or more separate and distinct crimes in a single count. . . . Although the Court made this finding on Count II, it was not dismissed. Instead, the government has until Friday to decide which of the two crimes charged (either the general conspiracy statute under section 371 or the terrorism statute, section 2339) to pursue. Obviously, the government will elect the more serious terrorism section.
The full text of the order is here.
Thus, while initially facing four charges in three counts, Padilla now faces two. It isn't at all obvious to me why this is not one count. It also isn't at all obvious why the judge chose Count I, rather than Count II or Count III to throw out. One suspsects it is because the judge previously noted that the indictment is "very light on facts," and didn't actually allege an effort to murder, maim or kidnap specific foreign persons, just support for a terrorist group generally.
It looks from the order like the most serious charge carried a sentence of 15 years in prison, down from a possible life sentence under Count I.
While it won't likely come up until sentencing, the other issue looming over any sentence is how much credit Padilla gets for time served. Clearly, he gets credit for the period from the time he arrived in Florida to the time of trial. It is unclear if he should also get credit for the time he was detained as an enemy combatant. The fact that being an "enemy combatant" and being a part of a terrorist "conspiracy" sound very similar, make it a plausible argument which is unprecedented only because, to my knowledge, no one has ever been held as an enemy combatant and then charged in the civilian criminal justice system with a crime.