Padilla loses on what will to many seem to be a technicality: his lawyer filed in New York when he should have filed in Charleston, SC. The majority does not reach the merits.
That is consistent with long-standing rules of habeas jurisdiction, but it's a darn shame the Court couldn't find it in itself to go the merits when they are so clear; the majoritydoesn't consider this case exceptional enough for an exception to the “custodian” rule, while the dissenters do.
Two of the five justices in the majority write a concurrence noting that if the government had been moving the detainee around to make jurisdiction hard, they would make an exception, but that this isn't that case — he's been stationary.
The appropriate district court will now have consider Padillia's case in light of the ruling in Hamdi, which ought to put him in a better position than he was the last time his case went to district court.
Four justices dissent, reaching the merits. More when I've read it all.