It’s is never more noticeable than in the last 2 or 3 episodes that the series has definitively split into two different storylines. We have Koku who is on his quest to rescue his love Yuna, while Keith is chasing after Gilbert for the death of his sister Erika. Lily has been rescued and is safe, thankfully, freeing up Keith to act on his own.
Keith assembles a gun he had stored in his apartment, and takes a train to a destination later revealed to be the site of the attack on the Jaula Blanca institution. He initially carries a paper cypher that he and Gilbert used to pass notes to each other in class, but Keith burns it up with his lighter while he’s waiting for his train.
As Keith is making his way towards the institution where the attack on Koku and Keith’s father took place, he calls Gilbert from his cellphone. The two men reminisce about their time together in school and discuss Erika’s murder. Gilbert also reveals that he was the one who proposed and led the attack on the Jaula Blanca institution, even going so far as to let Minatsuki (Laica) kill Keith’s father. The purpose of the attack was to actually kill Minatsuki, who was created as a collection of replacement parts for Koku. I’m not quite clear on what the intent was – maybe death to Koku if he needed a body part replaced and couldn’t get it?
But why kill Minatsuki? He was special in that he was the only Reggie who was able to be stabilized, and his body was able to keep Koku’s eye without rejecting it. Gilbert says he wanted to kill Minatsuki because the government and military would have killed him if they’d learned that he existed. Ok…?
As Keith walks in front of the door and stands in front of Gilbert’s projector (the latter had been watching old movies showing scenes from the attack and his years with Keith in school), Gilbert chilling says that he will never be happy because he can never stop killing; he must “kill to live.” Gilbert tries to draw parallels between himself and Keith, in that Gilbert has an insatiable drive to kill, just like Keith has an insatiable drive to study, just like his father. Keith isn’t buying the argument, of course.
As Keith and Gilbert inch closer to their final confrontation, the RIS team has crammed into a car and is racing up the mountain towards the Jaula Blanca Institute where the attack took place. Eric notes that it’s the location where Erika’s body was dumped, not where she was actually killed. Now that we know about Gilbert’s secret lab, it’s presumed (at least by me) that Gilbert killed Erika on that cold, stainless steel table before taking her body to dumped up in the hills.
The other main plotline going on is that Koku is going after Yuna. He follows Keith’s instructions and uses the updraft to fly up to the 
Moby Dick. Once onboard he fights off against Minatsuki – or at least the man who’s been portrayed as Minatsuki all this time. In reality this person was also just a Reggie, and he’s finally starting to degrade and go mad. He fights against Koku but loses, remembering his origins as his life passes in front of his eyes.
The real Minatsuki is the man named Laica, the man who has Koku’s other eye. Both eyes have the ability to re-write a person’s memories, and it’s Laica’s eye that brainwashed “Minatsuki” into doing his bidding. I’m guessing that this Minatsuki was the target of the attack on the institute.
After the Reggie disintegrates into dust Koku goes looking for Yuna, but we see that Laica has taken her unconscious form (“Minatsuki” had choked her unconscious earlier) and put her on a helicopter. Laica rigs the Moby Dick to explode with Koku onboard.
Laica takes Yuna to a place called the Jetblack, where the infamous tablet with the glyphs and inscriptions is located. Laica believes that if he can kill Koku he will be a new, immortal leader of the world, and thus everything he and Koku are doing is merely prophecy. Everyone is following the role laid out for them. It’s an easy excuse to believe in when you’re planning to come out on top, no?
Laica stabs Yuna in the stomach and Koku, who has survived the Moby Dick crashing and burning to the ground, rushes to the Jetblack. Earlier in the episode his hair and Yuna’s hair both “synchronized” and turned silver, and it seems like this gave them some kind of connection. Koku can now feel when Yuna’s in pain. Knowing Yuna is in danger, Koku hurries to Yuna’s side. But will she still be alive when he gets there?