Here's my theory: After FR, Venjix had his software scattered in space, after a space shuttle launched into space he attached himself into it's CPU and passed himself through the computers. He kept a low profile but secretly building an army by controlling computers and hard drives. He eventually created his army of machines which carried out plans on attacking Earth after Venjix hacked into the World's defense system. After General Crunch is destroyed, his robotic parts are salvaged and used as the new body for Venjix making him, Yogoshimacritein.
I know, pretty long winded.