The article didn't say what they were looking for, but I recently read that there are 1.5 million hack attempts on the Pentagon servers every year and they are they are going to start going after the hackers aggressively. The server that they want is probably either part of that sweep or related to a terrorist organization. It is too bad that they had to take down several unrelated sites in the process.
"Democracy is two wolves and a lamb voting on what to have for lunch. Liberty is a well-armed lamb contesting the vote." -- Benjamin Franklin