Earth Defense Force 4.1: The Shadow of New Despair. Here he is shown to invade a nest on his own, supposedly taking out the first wave single-handedly (although the camera feed failed during this period of time, and thus this is debatable.) He then boards a Depth Crawler and moves further into the nest. However, he has vastly underestimated their numbers and the Depth Crawler is destroyed. Despite this and multiple contusions and acid burns brought on by Ant attacks, Honda survives only to find himself abandoned in the tunnels. Growing scared and lonely, he adapts the EDF battle shout to his own purposes.
Later he is revealed to have survived, yet he is vague about the events that had transpired, only inferring that something recently happened to him.