The highest Level user of a Windows machine is called the Administrator, while on a unix/linux device it is called root. This is where the rootkit gets its name from.
A rootkit goes to the lowest level of the OS and modifies its kernel. It becomes a part of the kernel and can therefore becomes invisible to the OS itself.Which means it won't be visible in the Task Manager also. This can help it from antivirus detection.
These days malwares are built with rootkits so that it becomes extremly difficult to remove them.
For example: Even if you do manage to find the malware and proceed to remove/delete it, it throws an "Access denied" error as it has become a part of the OS itself.Even the Adminstrator doesn't have the privilege to remove it.
You can mitigate the installation of a rootkit by:
Even if it gets past your defences and you manage to find it, you would need a very specific root-kit remover for that rootkit.