If you need to monitor a Microsoft windows server without deploying a SCOM agent, you have the option to use an agentless managed agent from within the systems center operations manager console 2012R2
It works by using a proxy agent to monitor your server. The proxy agent is on another server, which will monitor the agentless server.
Follow this guide to monitor windows without a SCOM agent on the server.
Open up the SCOM 2012R2 console and click on Administration. Right click on Agentless Managed and select Discovery Wizard, which will bring up this window
Select Windows computers and press Next
On the next screen you will need to choose your discovery method. You can scan the entire domain for all your windows based computers or choose the option for an advanced discovery and select Servers and select your management server from the drop down menus as below
On the next screen you can either scan the domain for all your servers without an agent installed or if you know the hostname of the server you want to monitor select browse for and type in the name of the machine as below
On the next screen you need to decide what credentials to use to scan the target computer. Either the selected management server action account or another user account.
On the next screen you will get the discovery results from the scan if it has found your server. Select your server and from the drop down menu under Management Mode, select Agentless
Press next and then finish.
If you now go back to the console and under Administration \ Device Management \ Agentless Managed
You should now see the monitored server. It may take awhile to report back its health