Kali, You need a working floppy drive, so after #2 below if you're floppy drive is still not working you need to get one. They're cheap and easy to install, just crack the case, undo the screws holding the floppy in, unplug it from the internal power supply, take out the old and put in the new. However the process is to take it out will be the order in which you put it in. Just reverse the procedure...
1. "quit..." if you can access the net get an XP copy of "msconfig". Download it, put it in the sys32 folder. Exit.
2. I'm going to assume here (you need to provide a LOT more detail on what sys you're using to do this, as well as the w2k machine...a LOT more) that you're trying to do this from the w2k sys. So, after the download and install into the sys32 folder, (steps/buttons/clicks) Start>Run>msconfig>startup. Now, uncheck anything that points in the direction of these utils. Click Ok/Save Changes (etc.)>exit>re-boot. That should do it for problem 1..
Note: if that doesn't work then you're utils have a registry entry that keeps reloading them @ startup...I'm not even going to begin to explain that one. You'll need a comp literate buddy to help you there.
3. Wiping out your root directory. You need a floppy so that you can download and use any of the aforementioned programs. OR, google "fdisk" get a copy on a floppy. Boot your sys and hit the key to access the BIOS. Find the boot order, enable first boot location as the floppy, save your changes, put the floppy in (before you exit the BIOS) and exit. Hit the F8 key and use the command prompt selection/choice/option. That'll bring you to a command prompt without loading windows. Change to drive floppy...usually a: so, @ the flashing cursor that you're now at, the keystrokes would be: "a:"(without the quotation marks) thats all, hit enter. IF, you're floppy is working, it should be if you follow the above. Type in fdisk and hit enter. NOW, if I were you and had limited knowledge of comps and the how-to's I would get a comp tech buddy to take it from here. Fdisk will obliterate any and all drives and any info on them. Additionally, fdisk is not a learn as you go, graphically pleasant command. It is a no prisoners taken DOS command in a command line environment. You want easy, get an external drive, one that DOES NOT HAVE anything other than w2k programs, commands, loaded into it. You format in anything other than w2k it AIN'T GONNA WORK! Rule of thumb with comps and OS's. You can go backwards (most of the time) BUT you CAN NOT GO FORWARD. Don't forget anything today was built/compiled from yesteryear. Or, in other terms Win7/8 can read/operate most XP and later windows os'....(w2k is a whole other universe though), BUT you can not use '98/XP/ME/Vista to load/operate the newer OS' software/programs/interfaces/etc.
Hope this helps or at least points you in a different perspective