The manuscripts were taken captive by E-106 Eta's unit under Dr. Eggman's orders, along with the Professors Pickle and Uncle Chuck. They were stored in an Egg Train bound for the Rail Canyon Zone. The Knothole Freedom Fighters managed to intercept the train and rescue the professors, but forgot to get their research. Later, the train arrived at it's destination in rough shape, but Dr. Eggman finds that the manuscripts were still aboard and intact. After deciphering them, Eggman learns about the legends of the Light Gaia and Dark Gaia, and how the Gaia Temples and Chaos Emeralds were crucial to restoring the world after it was broken apart by the excess energy of the Super Genesis Wave. (StH: #256, #257, #258, #259)