The Third: Vol. 3 Gravestone continues Honaka's story, but it goes in a strange direction when she and Boogie are asked to track down a disturbance in the middle of the desert and the resulting odd behavior observed in the sand dragons. All four episodes on this disc follow this mission which seems fairly straightforward, that is, until they are approached by Paife, a teacher who seems to have a less mainstream side job, mercenary. It seems that Honaka's client has hired Paife to tag along and observe the Jill of all trades and make sure she actually does her job.

As the party approaches the center of the disturbance, it seems The Third know exactly what the issue is and they seem to be a little scared over it. In fact, they are planning on activating a forgotten space weapon left over from The Great War to put a stop to it. Combine that with Iks' reemergence and his desire for Honoka, Boogie and Paife to turn back, it gets pretty obvious that there is something strange going on.

Eventually, Honoka ends up revealing to Paife her blue eye and unusual nomadic past, and, very grateful to Honoka, Paife seems to accept these oddities. When the troop finally makes it to the source of the disturbance, they discover that it is another long forgotten weapon, named Gravestone, left over from The Great War, and it has been reawakened by Iks' arrival on Earth.

The Third: Vol. 3 Gravestone not only introduces Paife, but it also once again hints that Honoka is more than she appears, possibly even more than Honoka herself realizes since it seems like Gravestone has been calling for Honoka. In the end, Gravestone's mental assaults will have Paife fighting a super powerful kid, Honoka battling against herself and Iks having a long sit down with the mind behind the Gravestone weapon. All the while, time is running out as The Third prime the Wormhole weapon floating up in space. If they attack while Honoka and her gang are in the area, it could mean an early end to the series.