How to completely erase 2003 emac?

If you are able to boot to the OS 9 disc you should have access to the Drive Setup tool, which you can use to erase / reformat the disc. After that install OS 9.

If you want to put a clean version of OS X on the machine you'll need an OS X installation disc that is compatible with your eMac. Using that bootable OS X installation media you can wipe and reinstall OS X.

As another user mentioned, Cmd-R will not do anything because that was implemented in later versions of OS X. Holding C tells the computer to boot from the CD drive, which it will try and do if you have a bootable CD/DVD in the drive.

The Mac OS X system had to come from somewhere; if you still have the disk used to install it, use that. If not, use the Erase Disk command in the Finder's Special menu under Mac OS 9, or erase it from Drive Setup.

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Is the OX9 system disk an original pressed CD or a burned one? The latter seldom worked properely in PowerPC Macs.

Note: Starting the machine while holding Command-R does absolutely nothing.

Expected behavior. Recovery was introduced in macOS 10.7 Lion after Intel Macs were introduced. A PowerPC eMac can run no higher than macOS 10.5 Leopard..

Have you tried booting into OSX by holding x key on startup?