My Microsoft.Identity.Health.AadSync.MonitoringAgent.Startup.exe was running at 99%.
Some research quickly tipped me off to the culprit. (https://social.msdn.microsoft.com/Forums/azure/en-US/e9b621f6-f38c-488e-8fcb-ff85d406f256/azure-ad-connect-health-sync-monitor-high-cpu-usage?forum=WindowsAzureAD) .NET Framework 4.7.2 was the culprit. Uninstalling the right KB depends on your OS.
- Server 2008 R2 - "Microsoft .NET Framework 4.7.2"
- Server 2012 - KB4054542
- Server 2012 R2 - KB4054566
- Server 2016 - KB4054590
I was dealing with Server 2016, so I uninstalled KB4054590, restarted, and the server seems fine.
My Azure Active Directory Connect is current at 1.1.819.0, released 5/14/2018. (https://social.msdn.microsoft.com/Forums/azure/en-US/e9b621f6-f38c-488e-8fcb-ff85d406f256/azure-ad-connect-health-sync-monitor-high-cpu-usage?forum=WindowsAzureAD)
I'll be sure to monitor the version history to see if when I go to patch next month, if Azure Active Directory Connect has been updated to address this.