Well, I'm guessing they deleted everything through FTP, in which case everything is gone, your gonna need to redo it, Download all the plugins you want and dont set the server as public, instead use groupmanager and set up everything yourself. You're gonna wanna make a group for admins and moderators and for default, and if it's offline get something like AuthMe to stop people stealing accounts. You might also want something like Precious Stones, even if you mod it to basics, to protect against griefers, I can config most of the stuff if you aren't sure about it, but you'd have to wait until i could get onto your server. Basically, if the hacker got on through FTP, and you have no backup, it's gone. sorry