One embodiment describes a control system in an automation system including a first portion located at a first vehicle, which includes a first autonomous module that autonomously controls operation of the first vehicle to perform operations in a first area based at least in part on a first target operation result while the first portion is in an autonomous mode; and a second portion located at a second vehicle, in which the second portion includes a second autonomous module that autonomously controls operation of the second vehicle to perform operations in a second area based at least in part on a second target operation result while the second portion is in the autonomous mode and a first command module that determines the first target operation result and the second target operation result based at least in part on a global plan that indicates a total target operation result.