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how big is the system partition?
Is it an ssd or hdd? If its an ssd, defrag won't run on it as it doesn't work with ssd. They use a different process that is done automatically by windows.
If its a hidden drive it won't show in explorer, as they don't have drive letters. Win 10 has 4 partitions on the drive C is on, it normally only shows one of them though. The other three are used for various reasons, System is used for booting windows and is always hidden.
Partition 1 - Recovery
Partition 2 - System - The EFI System partition that contains the NTLDR, HAL, Boot.txt, and other files that are needed to boot the system, such as drivers.
Partition 3 - MSR...