I-Machines operate by sing the Mind Trance (MT) system, which transfers a human pilot's mind into the robot to facilitate activities.
Episode 2 ends with the Excavators verifying the Orichalt recovered by Ido and Maya, only to find a girl among the ore.
In Episode 4, Ido reveals that the reason he has no memory of his life before becoming an Evertrancer is because, when he first gained consciousness, he had an ID score of ID-0. This is also the reason for his name.
The MT system allows pilots to use I-Machines as naturally as human bodies.