Pentagon reports were a bit premature, and lacked a few key details about the hijacking. I think I've managed to piece most of them together.
When the crew overpowered the pirates and took one of them into custody, the pirates managed to take the captain of the vessel hostage. The crew tried to negotiate for the captain with the last pirate, but the trade never happened, and the other pirates escaped on a lifeboat. The USS Bainbridge, a missile destroyer, has arrived on scene with FBI hostage negotiators to seek his release. The Mearsk Alabama is on its way, under armed guard, to Kenya to deliver the aid supplies.
I'll try to keep you updated on the fate of the captain, as well as that of the pirates.