Summary:

We get an extended recap instead of the opening credits, giving us a synopsis of the series so far. After this, the carrier is about to arrive in the harbor of an island known as Nirai Kanai. At the same time, another ship is arriving at the island, as we see the Captain of that ship talking to an odd looking man in sunglasses and a flat top hat. We also see a red haired girl on the carrier, the same one seen for a moment in episode 1 when the operation was initiated. Finally we get a glimpse of the Commander's second in command, Souichi, a young man onboard ship.

On board, Ayato is getting a checkup and blood test done. Haruka watches with obvious interest as they draw his blood - it is red and she seems relieved. Just then, the Commander of Terra arrives in sickbay. He tells Haruka to look for the cat, then tells Ayato that his watch's time is wrong and he needs to adjust it. As we move around the ship, we see that it is carrying the RahXephon.

Later on the bridge, the Commander of Terra is told to hand over the RX to the Earth Federation's Mulian Technology Labs by the other captain. When the Commander asks about Ayato, the Earth Federation Captain says they have no interest in the boy; that they have enough Tokyo Jupiter specimens.

Meanwhile above decks, Haruka is looking for Buchi the cat. Ayato asks about what he was told by the Commander about time difference. Haruka shows her watch explaing that it's not just a time shift to the outside world - that time in Tokyo Jupiter is going slower than outside world. They are being watched from cockpit of nearby fighter (looks like one from battle in the first episode). Haruka tells Ayato to go on ahead.

The pilot of fighter is another woman, and she's upset with Haruka for not telling her about the operation. She wants to know why all her wingmen died to get one boy out of the Mu area. She also wants to know if Haruka knew about the operation before Haruka got her drunk, and when Haruka doesn't give a straight answer, we hear the sound of a punch.

Inside the ship, Ayato sees a barber pole near one of the rooms, then meets the redhaired girl (RHG), who keeps saying "Rara?" He says he thought it was weird that the ship has a barbershop. She mentions that the red, white and blue barber pole was once a medical symbol, with red and blue representing blood vessels - she wonders aloud why there are two colors of blood vessels since human blood is red. Just then, she asks Ayato to help her put on her vest, which she is carrying one hand. Of course, typical feelings of embarassment from Ayato as it's a close fastening job. After, she grabs his hand and says "Come on Ollin, let's go." He asks what an Ollin is, and she tells him "Never mind."

On deck, they notice the RX being taken to the other ship. The RHG seems surprised, Ayato is upset. Just then, the sunglasses/hat man comes up and explains that what they do with spoils of war is none of Ayato's concern. Ayato asks what his name is and...

We flash to the bridge where Sunglasses/Hat explains that he is named Isshiki Makoto and he works with Terra. Ayato asks about RX and the Commander explains it is going to Federation Research. Souichi notices that Haruka has a black eye from being hit earlier (they were both on the bridge also)

The Commander tells Ayato that he cannot claim ownership on the RX, and when Ayato yells and tries to fight, Haruka moves to stop him. The Federation ship leaves with the RX. Ayato asks if he will be transferred like the RX. The Commander says not at this time, but it is their right to do so. Haruka seems worred, says she'll brief Ayato on his situation. All the while, the RHG watches RX sailing away and speaks cryptically of matters (this happens often with her, for me to explain most of it would be difficult, as most of it is riddles and meaningful statements of code.

Haruka is in a room saying that the Commander just wants Ayato to adjust, Ayato says that people on outside don't see the Tokyo Jupiter people as human, or at least not as equals.

Meanwhile, in med lab, the doctor says that Ayato has the Mu Phase in his blood. They don't think he's a Mu, but the commander decides to treat Ayato as if he is for now. We flash back to the room, where Haruka asks Ayato if he thinks she's that way also, he says "No, not you." She tells him "Then who cares what the rest think?" As they look at each other, Haruka is summoned to the bridge. As she leaves the room, she notices the room seal behind her, and she knows he is being locked in and is upset. She goes to the bridge and tells her superior to let Ayato out or let her in, but the commander will not. In addition, if the door is forced, it will explode. They explain the test to Haruka, saying that Ayato has the Mu Phase, but she says he doesn't know anything and vouches for his cooperation, yelling that he is human. The others cannot agree - they point out on a camera that while he could be reading up on his situation on a computer in his room, instead he is drawing. The Commander says that his personality makes no sense. The picture Ayato is drawing is the same as his painting - a picture of a girl on a cliff who appears to be Reika. Just then, the RHG walks ont he bridge holding Buchi - she tells them the Mu are coming.

A sub is attacked first and destroyed, then the automated defenses are tried to stop the Mu, The Dolem is approaching Nirai Kanai and the female pilot wants to launch, but her ship not ready. Automated drones called Eidolons fight and fail. The Dolem comes to the base, surfacing underneath it and pushing its way into the base. As it pushes its tentacles into the base, they seem to seep through the metal of the walls and floor.

The tentacles move around the RHG, but she steps back one step and they come no further. Ayato is trying to get out door of his room, yelling for Haruka. He thinks Haruka betrayed him in locking him in and that he could be killed. Just then, his picture glows, and it looks like Reika in the picture is moving. On the Federation ships, the RahXephon gets up, breaks free, and flies back towards Nirai Kunai. The RHG's eyes begin to glow red. As RX approaches, Haruka (on the bridge) realizes it is coming for Ayato. RX lands in base puts hand on the floor. The RHG turns around and somehow can see (through the wall) Ayato looking at the girl who looks like Reika. His picture seems to have come to life around him. When Reika turns to look at Ayato, his eyes also glow red as he says "Mishima." She reaches out to him and they clasp hands. Suddenly, Ayato is teleported to the RX. The RX rises and easily crushes the Dolem, carrying it outside the base and destroying it in seconds, showering the area in blue blood.

Some time later, the captain of the Federation ship is saying that Terra must have stole the RX, but the Commander suggests that perhaps the captain should show his orders to the RX. They decide Ayato cannot be confined as the RX lands on Nirai Kanai in a pool near the Terra base on the island. There, a scientist in glasses is awaiting it. When sees a glowing and sleeping Ayato come out of it, he says "Welcome back, Ollin."

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A lot of good things to get a grasp on in this episode. A variety of different characters are introduced, among the most important being the Commander of Terra, Quon (the RHG), Souichi, and several others. There's not a lot of development on Ayato's part, other than his seemingly odd possessiveness of the RahXephon - it doesn't seem to scare him at all that he's seemingly bonded to this odd humanoid craft. Haruka gets a lot of development this episode, as we learn more about the operation which was sent ostensibly to retrieve Ayato.

Many of the characters in this episode will see their roles expand in the next few episodes on Nirai Kanai.

We get a slightly better explanation of the time difference between Tokyo Jupiter and the outside world, although much of that has not been explained yet.

It might seem odd to mention this, but Buchi the cat seems to serve no purpose. His role would seem to be to show the humanity of certain characters, but I would suggest that a cat isn't necessary to do that. I don't think the cat was suppossed to be the token fluffy animal, because quite frankly, it's not drawn in a very cute manner. Mostly, Buchi seems to be some sort of foil for Haruka, although her humanity has not been in question yet in this series - she very clearly displays her emotions at times.

Repeat after me: Quon is not Rei from NGE. Quon is not Rei from NGE.

The island will be revealed in the next episode, as we learn more about the organization Terra and the components that it is made up of.