Coming into Final Decision, Honoka, Blue Breaker, Iks, Paife and Bogie are trying to infiltrate a strange science facility that has been overrun by nanomachines being controlled by a rogue member of The Third known as Rona Fauna. In fact, there seem to be multiple Rona's since Iks and Paife have just defeated a creature that looks a lot like her at the opening of the facility, Honoka and Blue Breaker are standing in front of one apparently in some sort of cryo-stasis and Joganki is being held captive by the one apparently controlling the entire facility (her lower half has been taken over by the nanomachines and she is given a decidedly serpentine appearance.
After their battle, Iks takes Paife back to Bogie so that she may recover, but the main focus of the first two episodes on this disc involve Honoka, Blue Breaker and their confrontation with the final Rona Fauna. Before the end, Rona and Honoka will realize that they have a lot in common, and are both seen as "defective" by The Third (Honoka with her blue eye and Rona with her... unusual abilities).
The last two episodes lead up to the series' finale. When the crew get back to town, they find out that Bogie's mechanic, Joey, was arrested for breaking the Technos Taboo (the law handed down by The Third to try and keep technology so limited that humans can't start yet another World War). Meanwhile, Iks decides that it is time to do whatever it was he came to Earth to do and starts a trek to a place known as The Steel Gorge. But this place is supremely off limits, and it has something to do with the Taboo, but we don't really know what (at first). When Honoka realizes that this might be the last time she see Iks, she decides to go with him.
Of course, The Third don't want anyone going near the place, so they charge Joganki with stopping the pair. But when Honoka shows that her newly awakened powers can easily overcome any foe The Third sends at her, Joganki escorts the unlikely pair to the bottom of the gorge that looks like a scar across the Earth.
While I don't want to reveal how the show ends, and what they find at the bottom of the gorge (or why Iks is really on Earth), I will say it is all really nicely done, and leaves open the possibility of a second series set in the same world. I hope they do further the plot, but would have no problem if the show just ended as it were, without the possibility of it getting ruined or simply running for too long.
If you've been following The Third, then this is the volume you have been waiting for. If not, then you definitely don't want to jump in here, but since the series is only six volumes long (including this one), it wouldn't take much to get caught up. The show overall is solid with great character development and a good mythos, it definitely ranks high on my top-anime list.