An earthquake hits a city and things start disappearing into the ground. On the boat to TERRA, Kim sees Ayato and Megumi arguing and teases them about going into work together. Kim introduces herself to Ayato and he tries to do the same, but she already knows about him and how he pilots the RahXephon. Ayato says he doesn’t pilot anything and he won’t do it. The TERRA crew watch a press conference on TV. Souichi comments that TERRA’s commander, Shirow Watari, is in a bit of a pickle. The press ask about how TERRA should be disbanded and its lack of effectiveness, and Shirow answers that no one should expect perfection. Reporter Johji Futagami asks about a Federation ship docking at Nirai Kanai and leaving as empty as it came. Jin says it’s a Federation matter and Johji says they were after something and says it was TERRA’s secret weapon. Shirow answers that it must be some secret because even he doesn’t know about it. Ayato comments on how some people don’t like TERRA and Haruka says they think the Mu will stay in Tokyo Jupiter if they are left alone. The alarm goes off and they get a visual of a city with a large symbol dug out of it. Shirow and Jin leave the conference and Johji wonders if hope was also in Pandora’s box. Souichi is made the acting commander and Itsuki explains the D1 Aria, a sound wave that is like a Dolem’s fingerprint. The recent Dolem’s aria matches one recorded 14 years prior in Australia. Haruka explains how the Dolem killed six million then, and Ayato is amazed because until recently he thought the total population was only 23 million. He tells Kim he can’t believe he beat a monster like that and Kim asks why he’s using the past tense. She says there’s more work for him to do but Ayato still refuses to fight because he’s not a part of it. Kim asks if he’s just going to freeload off them and he says he’ll work, but won’t fight. Kim asks what he is good for and he says she knows nothing about him. Kim says she does know how the world works and he doesn’t. Haruka tells them both to stop and Itsuki says they should stand out in the hall with buckets of water. Later, Megumi tells Ayato how Kim’s parents were killed in Australia while they were on vacation, and that’s why she works for TERRA. Kim begs Souichi to let her help so she can have her revenge but Souichi refuses. Itsuki enters and Kim leaves, but not before Itsuki gives her the aria data to give to Intelligence. Shirow and Jin meet with Ernst Von Bahbem and report that the Federation is letting them keep the RahXephon under surveillance and will only use it in emergencies. Shirow says it’s thanks in part to the Bahbem Foundation and they’re grateful for it’s support. Kim listens to her walkman on a train and remembers when her parents died. Quon appears and has a listen, and Kim admits she took the aria data without permission. Ayato boards the RahXephon for a test and reiterates that he won’t be fighting. Itsuki says he understands and Sayoko says he’d be mad if he knew the truth. Itsuki says he hasn’t lied, but if Ayato doesn’t ask, he won’t say.
Kim remembers when her parents first died, and how her guardians only agreed to look after her for a few weeks, not the rest of their lives. A package arrives and it’s a music box her parents sent before they died for her birthday. Kim says it was their last message and then realizes that the aria is also a message. She tells Souichi that the aria’s waveform is also the pattern of the cities attacked by the Dolem. Souichi says that the military wouldn’t deploy on this alone, but says it’s a good thing he’s in charge. She thanks him and kisses him on the cheek. Military forces set up in a city and Elvy wonders why her and Haruka are there. Elvy thinks Haruka is still worried about Ayato and Haruka says she heard about Elvy’s transfer request. Megumi asks Souichi how he got the military to agree and he says they think the Dolem is after the RahXephon. The Dolem Ritardando appears and sinks into the ground, pulling tanks and streetlights down with it. The RahXephon jumps at it but it disappears. Ritardando appears under it and sends Ayato flying into a building. Ritardando repeatedly slams into him and Ayato goes into a frenzy of punches. He remembers when Kim asked of he wanted to revenge, and he stops, saying he doesn’t. Ritardando sings, and the RahXephon starts sinking into the ground. Ayato calls for help and grabs onto some powerlines. Kim thinks back to before the mission when she asked Ayato why he decided to fight. She asks if he wanted revenge too or if it’s sympathy but he says it’s because he can and that there has to be a reason he has the ability. In the RahXephon, Ayato sees Reika and she takes his hand and pulls him up. The RahXephon flies out of the ground and charges at Ritardando. It throws it into the air and Ritardando charges again. The RahXephon just stands there as Ritardando is destroyed on impact. Jin tells Shirow the mission succeeded and that Souichi did an excellent job. Ayato looks in his sketch book and sees a thank you note from Kim. Kim wishes herself a happy birthday and destroys the aria data.
Some good character development in this episode, namely with Kim. Revenge was her motivation, but once it concluded she’s able to move on with her life. She also helps Ayato finally make his decision to fight with the RahXephon though his reason was that “he can,” which is standard mech pilot reasoning. The Dolem in this episode may remind some of Leliel, the 12th angel from Evangelion in the way that it sucks things up, but the similarities pretty much end there. The RahXephon once again struts its stuff, this time beating a Dolem by just standing there. Now that Ayato has decided to fight, there will be many more battles to come.