If he doesnt know the password to any of the accounts that have administrative privilages than you have a serious issue. It could be that the system is missing critical updates (there have been a number of volunerabilities that allow for privilage elevation) or it could be that your system has been comprimised and he is aware of it (i.e. trojan/back door).
Whatever the case you know the system has been comprimised, it's going to be next to impossible to ever consider this system "clean". At the very least I would suggest a very thourough audit of the software and configuration and to change the passwords for all your accounts that have any level of privilages on the system.
I would also make your knowledge of the situation clear to him as well as making sure he knows that this kind of behavior is absolutly not acceptable (assuming it is something he did). If this is a personally owned system I wouldnt allow him to use it any more; if this is an institution I would suggest formal diseplenary action.
I take security breaches very seriously, if this were one of my systems his job would now be on the line.