The being that Cloud and his party faced at the end of their quest was not actually Sephiroth, but one of his clones that he had groomed to guard his body during his transformation into a god. After Meteor was repelled by Holy, Sephiroth awoke and realized that his plan had failed. No longer having the black materia he decided it would be best to find somewhere that materia was untapped and unknown. Gathering his power he opened a portal that by chance led him to present day earth. He stepped out of his portal right into the midst of a pitched battle between GI Joe and Cobra. Unfortunately, some new recruit greenshirts were the first to open fire on him, believing him to be a new Cobra. The stunned Cobras stopped fighting and watched as he decimated the Joe's ranks. He called lightning and small meteors from the sky, he caused some of the greenshirts to burst into flames and others to freeze in their tracks. He cut down any who got close to him with his giant Masamune blade. General Hawk called a retreat in order to find out any information on Sephiroth and find an effective way to deal with him. The Joe casualties were all greenshirts and they had plenty of wounded. After witnessing his awesome power, Cobra Commander approached him in order to offer him a place within the Cobra organization. Sephiroth decided that Cobra's technology would be useful to him in his search for materia, and that Cobra Commander and his army would make excellent pawns. Of course Sephiroth keeps his true intentions to himself.

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