Well tonight we're going to party like it's 1999.
This article was originally published right before the issuance of MS-DOS 2.0. That was not even near the '90's yet.
By the time this was captured in the year 2000, the MSDOS.SYS file had already become almost a dummy file of few bytes in Win9x.
The DOS OS itself with only the native commands is basically contained within the IO.SYS, MSDOS.SYS, and COMMAND.COM files, originally written in that order starting at the first working sector of a formatted floppy disk so it would boot.
On a hard drive the 3 files would have to be written starting at the first working formatted sector of an actively flagged primary partition, and a proper master boot record needs to be on sector 0 (along with a valid partition table) if any boot files on that HDD are to be recognized by BIOS to begin with. Otherwise it would not boot.
IOW once the volume boots you can do things like copy files and list directories, but if you want to edit files or format other volumes you needed more than just the 3 OS files. You needed the additional OS apps like EDIT.COM and FORMAT.COM on your floppy so they would be there when you needed them after you booted.
Once booted, the SYS command could be used to properly write the OS to a target volume, so you needed SYS.COM for that.
And by W9x, the three DOS OS files would no longer need to be right there at the start of the volume (as if they were the first things copied to the volume), and DOS FDISK would handle HDDs of hundreds of GB even though each FAT32 partition was only supported up to 32GB.
The undocumented FDISK /MBR command executed from an A: or B: (floppy) prompt would simply write a fresh bootable DOS master boot record to sector 0 of C: (what should usually be considered) your only HDD on the mainboard. Without disturbing the partition table there.
The SYS command also replaces the Volume Boot Record (bootsector) of the target volume with a fresh DOS bootsector as it freshly (over)writes IO.SYS, MSDOS.SYS, and COMMAND.COM into the file system.
So you want to make a zeroed HDD boot, first boot to a DOS floppy (USB stick will do):
Run FDISK and create a primary partition (bigger than 512MB) smaller than 32GB on the fixed (HDD) disk. Make the partition Active.
(Alternatively you could use some other way to make a suitable partition, like Linux or a modern Windows version but the resulting "geometry" of the disk layout may not be the same or fully recognizable by DOS, which can affect the bootability. Sometimes with Linux or Windows, the older the version the better. Outcomes can also be surprisingly interesting when certain sectors of the HDD are not exactly zeroed beforehand. AMD also not quite the same as Intel, nor old Seagate identical to WD.)
Now you've got a partition table on sector 0 with one primary partition marked "active" so the BIOS will boot to it.
Run FDISK /MBR and it silently writes an MBR to sector 0 so the BIOS will REALLY boot to it.
(You may need to manually copy a working MBR to the first 440 bytes of sector 0 if the FDISK /MBR command does not do the trick. The MBR is supposed to be generic for DOS and a Linux version like MBR.bin from the Syslinux project can be copied bytewise with binary tools. Newer Windows will also upgrade the MBR but it will still boot DOS (or Linux) afterward from a submenu.)
All other sectors are still unchanged.
Run FORMAT on the partition and I would always suggest labeling it as to HDD/Partition# when done. 11 characters max.
Now you've got something other than zeros in places other than sector 0 of your HDD, but still no data actually located on the formatted volume yet.
Run SYS on the formatted volume and it properly writes the 3 critical DOS OS files to the volume.
Power down, remove the floppy or USB device.
The HDD should then boot DOS according to mainboard BIOS priority.
Add W9x to the same FAT32 volume and you still get a DOS boot entry on your Microsoft boot menu for when you want plain DOS.
Install WXP to a different formatted partition (even FAT32) and your old W9x/DOS volume still can boot when desired as a submenu of the NT5 NTloader that replaces the DOS bootloader on that active partition.
Then with Win10 (non-UEFI setup) on a third (NTFS) partition you can have an NTLDR submenu within the replacement NT6 Bootmgr and boot any of the above.
Note the volume you installed the new Windows version to does not become active itself nor contain any boot files. By default additional boot entries are made to the established active partition. Even logical partitions containing OS's can be booted this way, according to OS version, from one of the few primary partitions you are allowed to flag as active.
BIOS only. Too bad with foolish-type UEFI or GPT, no DOS for you.
Also remember with bare-metal DOS/W9x and audio/MIDI (no USB), no latency for you either.
Even on dog-slow PC's.
Things like that.