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Open the below path in the  target server,

\\scom01\c$\Program Files\Microsoft System Center 2012 R2\Operations Manager\Server\AgentManagement\amd64

install the package name MOMAgent.msi

Specipy the Management Group Name(refer to SCOM 2012R2 (2) new  installation) and Management Server

After installed Agent, copy MOMCertImport.exe to C:\  from the install media(SupportTools\AMD64\)

Apply a ServerAndClient Cert for target server,mark the private key exportable

Export this Cert to the target server

Import this Cert to the target server

Open CMD and run as administrator,type MOMCertImport.exe

select the Cert imported before

Restart  Microsoft Monitoring Agent service

Goto the SCOM console,  config the Security :Review new manual agent installations in pending management view

Goto pending Management,click approve 

You can see the target server state will change to Healthy  after a few minutes

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