Recently I had problem with SCOM agent. Shortly it crushed totally SharePoint 2010 frontend server. To find out more you can read about it on this post APM feature in SCOM 2016 Agent may cause a crash for the IIS Application Pool running under .NET 2.0 runtime.
One of the solutions was to install agent manually without installing APM feature. Before you do anything first copy installation of MOM agent or complete SCOM installation locally on PC. I copied everything in C:\SC 2016 RTM SCOM folder. This is the short description of command use to do it. It is used when you don’t have AD integration enabled and you use Local system account as Action account
%WinDir%\System32\msiexec.exe /i "C:\SC 2016 RTM SCOM\agent\AMD64\MOMAgent.msi" /qn USE_SETTINGS_FROM_AD=0 USE_MANUALLY_SPECIFIED_SETTINGS=1 MANAGEMENT_GROUP=scom-hteronet MANAGEMENT_SERVER_DNS=scom2016.domain.com SECURE_PORT=5723 ACTIONS_USE_COMPUTER_ACCOUNT=1 NOAPM=1 AcceptEndUserLicenseAgreement=1