Runners are seen in the Animatrix short Matriculated. They are a type of advanced Machine scout/patrol unit capable of multiple transformation modes. Runners are so named after their function to run over ground instead of the typical hovering that most of the Machines use, since they have no capability to hover and are bound to the ground with their movements. They are even able to swim and mostly appear in pairs.

Runners are able to transform to adapt to the needs of the specific situation and environment. For instance, a Runner is able to transform from "a tentacled insectoid that walks on four spider-like legs" to "a form resembling a humanoid that slides along with its head tentacles and uses its legs as arms tipped with huge claws". Runners are equipped for close combat with these claws, but when they are facing a larger group of targets or spot rebels they can drop off a tracking beacon that alerts the nearest Machines and retreat, leaving the dirty work to the more powerful Sentinels.

Alexa, a member of a small band of rebels on the surface, leads two Runners to their base so they can be converted to the side of humans. One Runner is killed by their guard robot, but the other Runner kills the guard. Alexa then blasts the Runner with a plasma rifle. They then plug the Runner into their dreamscape where the Rebels attempt to convert the runner to their side. It is during this reprogramming that the Sentinels attack the base. When it finally reacts, everyone and everything is dead except for Alexa who was knocked out. The Runner hooks her and itself into the dreamscape, where Alexa panics and dies.

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