There were chapters that explained Ziggy's origins (don't remember when). I think the cause was a giant explosion caused by all those explosives from the other guy who studied under Ziggy to learn Gravity ethergear.
Anyway, explosion and almost 20.000 years later, for whatever reason, robots find the remains of Rebecca and Shiki and that Shiki had somehow retained a minuscule bit of life and the robots decided to give him a mechanical body. He couldn't pronounce Shiki right in the new body and came to be known as Ziggy. And Rebecca's body hadn't decayed and was thus experimented on because there were still ether signs in her body, her ether was used to make the Eden's Zero and make it able to travel through time to our present. And then, as we saw earlier, Ziggy was leaving and that Rebecca couldn't take it and somehow became the Chronophage.
And this is about all I can recall from that part of the plot.
wait.. 20 THOUSAND YEARS LATER???! WHY IS REBECCA IN THOSE TUBES? WHAT JUST HAPPENED Σ(っ°Д °;)っ