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Initially windows defender was disabled for some reason in Windows server 2016. I enabled it from gpedit.msc by disabling "Turn off windows defender".

When opening Windows defender, it shows real-time protection "disabled". I went to settings and enabled realtime protection but still defender shows it is disabled. Please see http://i.is.cc/tmZNGl.png

I followed the suggestions in this post, but no luck.

The server had few malware which was removed using Microsoft security scanner and online eset scanner

sfc /scannnow finished without any errors. I'm out of options. Please help.

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Leave it off and install a real AV.

Seriously though, if you had malware you probably had other stuff installed. Some of those are designed to disable and stop anything that could remove them from doing so.

Reimage the server is your best bet.

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