Summary:

The RahXephon has hatched from the gigantic egg and taken Ayato inside of it, as Maya and the agents look on. Ayato says "Mother" aloud, but is surprised to hear Maya's (his mother's) voice in his head, saying "So, you've awakened." Apparently she can communicate telepathically. She tells him that she has been waiting for him to "awaken". Meanwhile, the military watchers who were with Maya detect an energy signature, saying that Dolem and the Xephon are syncing. At that point, one of the Dolems (I don't remember which) crashes through the wall of the Shrine of Xephon, which shatters the ground under Maya and the agents. Surprise surprise - Maya can float in midair and does so, floating up to the second Dolem that enters as she utters "Come Ayato..."

As Sunglasses runs up the Shrine, Maya notices Reika on the RahXephon's shoulder and is shocked by her appearance. Meanwhile, Sunglasses yells "Ayato, don't do it!" as she gets near. She is about to get caught in an avalanche of debris caused by the Dolem, but Ayato reaches out (via the RahXephon) to block it. The shock knocks her out, but the RahXephon surrounds her in an orb of light and picks her up, all the while yelling out a multitone yell, which lifts it into the air. One of the Dolems follows it up, and the two titans stare at each other in the Tokyo skies. While this is going on, Maya (on top of the other Dolem) watches and says "Ixtli... of course..." while brushing away the blue blood.

Reika is still on the RahXephon's shoulder, saying in a multitonal voice "Time to sing, Rahxephon... Sing the song that is forbidden.... Sing, so that someday all will become one." Ayato can hear her inside, and turns the head of the RahXephon to see her on his (RahXephon's) shoulder. The Dolem attacks, hitting the shoulder Reika is on. As Ayato looks for Reika, he sees only her shawl falling, and he screams in defiance at her apparent death. The watchers note the scream. The Dolem fires again, this time dead center, but Ayato's yell causes a shield to block the blast. He reacts violently, putting his hand to the Dolem's neck, crushing it. At the same time, a woman in the watchers' center reacts like she is being choked. Above the Rahxephon, a circle of light appears as the Dolem is dying, and when it does die, the choking woman also vanishes. The circle of light sucks Rahxephon in, and the watchers say he has "lept the barrier... with.. the Ollin..." Maya watches and seems undisturbed - as she puts it, Ayato will return to her, with Ixtli.

Ayato awakens on a beach, staring up at the RX (what I'll call the RahXephon from now on). As he looks at the horizon, he notices and orange-red barrier nearby, taking up a good portion of the sky. Nearby is an abandoned boat, which Sunglasses emerges from, where she was apparently search for a transmitter. He asks her what the barrier is, and she answers "That's Tokyo Jupiter... well, that's what we call it." She tells him it was his entire world until this morning, but Ayato is confused. She starts to look for pursuit, and as she does on the boat, Ayato causes her to fall towards the water, as he jumps after her, grabbing her in midair, making her blush.

Later, wet and tired, the two look to dry off. Ayato says he thought the outside world was destroyed, but she says that's what he had been taught, but that it still exists and he shouldn't believe everything he's told... that he's not a child. They go to find dry clothes and food to eat. The town is overgrown, like its been abandoned for some time. In a nearby store, Ayato finds some HIDEOUS purple clothing, then notices a phone covered in dust. As he tries the phone, Sunglasses says that he's wasting the time - there's no power or working phones. Sunglasses emerges in new clothes, but tells Ayato to change into something better.

They grab water and food from abandoned store, and Ayato says they should get some boxed stuff as she is only looking at canned, but she says he'll get sick. Ayato says he thought that the food was good for three years from date. The box says the date of expiration is 8/16/2015, and as she looks, she mumbles "That's right, you don't know yet...." She says they need to go back to RX (thus telling Ayato the name). That night, they listen to a radio broadcast about the olympics, saying that last Olympics was 2024.. shocking Ayato, as he says he was born in 1998, and he's only 17. She looks at her watch, does some calculations, and says it's 10th of Nov 2027. He asks if she's from the future, which causes her to laugh.

She tries to explain that its really 2027, but leaves it at that.
He asks if everyone stil exists inside the sphere, and she tells him they're all okay, which comforts Ayato.

The next morning, she awakens to find Ayato gone. He is walking around, seeing the abandoned city remains and the overgrowth. While walking in one area, he hears a payphone ring. When he answers, he hears his mother on the other end. She says to him, "Be Careful... the ones that wrecked our city, they'll try to make you forget about me... they'll compel you to hate me and make you believe horrible things about me.. Be strong (the voice breaks up into foreign tongue, like Latin here)" Ayato yells asking about the blue blood, but gets no answer and runs away from the phone. He runs to the edge where the land ends before the barrier of Tokyo Jupiter... it looks like the barrier just appeared, cutting off the area, breaking land, bridges, pipes, etc. Sunglasses rides up on a bike behind him, says it's 10 KM from there to barrier. She says they think the bottom is also hemispherical, so you can't just tunnel your way in. He says he could go back, but she says that he can't.. that it took too much energy for them to enter. Ayato goes to the bike, takes it from Ayato, and tells Sunglasses to get on... he'll pedal.

On way back, she says she'll have to call for a pickup somehow. While searching for a transmitter, they find a cat roaming in the ruins and take him along to feed him. Ayato asks her what she's going to do with him, and oddly, she asks him if she can keep him. Hearing a plane overhead, Sunglasses turns the boat into a bonfire, signalling the jet. Much later, they see a ship coming to pick them up. She tells him its a carrier belonging to TERRA, an "Earth Federation Anti-Mu strategy group" and that she works for them as an intelligence officer. She says her name is Shitow Haruka. End of episode.

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We have sort of a reverse Matrix going on in RahXephon, or so we are led to believe. Is the inside world of Tokyo Jupiter the real remnants of an alien attack, or is there really an outside world. Who is lying - is it Maya or is it Sunglasses? And who/what is Ixtli? There are so many questions to answer, and we've just barely scratched the surface.

Assuming this is a reverse Matrix, then what is the significance of the time difference between Tokyo Jupiter and outside? The RahXephon would seem to indicate that all is not false inside Tokyo Jupiter, so what is being hidden from Ayato?