Can you restart the server in safe mode with networking? Do services work there? If not, sounds like your system is beyond repair and will need to be reinstalled. Were there any critical services like DHCP, DNS running on this system and not mirrored on the other DC? If so, you need to find a way to backup the information so it can be restored at reinstallation.
Sometimes with a trojan (especially a rootkit), it is much better to reinstall anyway as you cannot be sure what system files have not been changed or modified. You should always have antivirus protection on a DC and keep patches up to date. The DC should also never be exposed to the internet.
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