Eggman fainting after finding out the treasure of Babylon is a rug and not the typical exploitable source of energy he usually goes for. It's actually a prototype Extreme Gear, but he fainted before that explanation came about.
In Zero Gravity, Wave does a bit of foreshadowing while Jet and Storm listen. When they bring their attention back to the Arks of the Cosmos they just got? Eggman somehow stole them both from right innfront of Storm and Jet and already began running away without anyone noticing until he flew by the window.