In order for Eon to create the Godmaker, he needed the Plumbers files on the Ultimatrix. These files could be found in the Plumber database, but the only way to get his hands on those would be to steal them from a Plumber Base.
While Ben Tennyson and Danny Fenton were occupied by Vlad Masters, who was causing havoc in Bellwood, The Alliance teleported the operative GIR to the Plumber Base stationed in Earth's orbit. While there, GIR downloaded the information Eon instructed him to retrieve from the base's servers, to the obliviousness of GoTro, who was meant to be monitoring the digital surveillance of the base. The Orion Squad were unaware of the intrusion, as the lifeform detector wasn't triggered due to GIR's robotic nature. After GIR duplicated two files from the mainframe, corrupting the originals, he left the base, cutting a hole in the side and escaping through a transporter rift.
GIR was successfully able to steal the Plumbers files on Ben's former Ultimatrix. With these files, Eon now had everything he needed to create The Godmaker, except the Hands of Armageddon itself. With this, his next move was to travel to The Keshawn Desert to obtain The Hands of Armageddon and to start finally building the machine.