I finally finished this.
Done mostly in Paint Tool Sai and then edited and finished in GIMP.
The origin of Metal X is an experiment done on the nano technology of the Galvanic Mechomorph. They combined it with a new super alloy that had characteristics that made it perfect for nano-machine research. The experiment went very wrong and it escaped. It hacked into the Galvan mainframe and found a file about the omnitrix and sought to obtain its power. He headed to the Codon Stream planet to find out what it could there. Azmuth had been waiting for it there and when it arrived he plunged it into the Codon Stream (Not before a long battle to be sure).
The Metal X was destroyed but in doing so it's nano structure was added the omnitrix's database as it's body was similar enough to that of Upgrades'.