Synchronization of multiple vehicles in an independent cart system to reduce spacing and increase throughput designates one of the movers as a leader and at least one additional mover as a follower, defining a chain of vehicles. A motion command for the chain is provided to a controller for the leader, and the controller generates a motion profile. The controller passes this motion profile to a controller for each of the follower movers. If the follower is unable to maintain the motion profile for the leader, the controller for the follower generates a message to the controller for the leader indicating a modification to the motion profile is required. The controller for the leader modifies the motion profile and forwards the modified motion profile to controllers for each follower. If all movers are following the modified profile, the controller for the leader may return to the original motion profile.