Today is part of Commander Kunagi's backstory, which makes this a compelling episode which doesn't overly rely on flashbacks.

SUMMARY:
The episode opens with a Dolem attack. Elvy and her squadron are attacking the Dolem, while it lashes out at the RahXephon, which attacks and slices apart it apart. A barrage of missiles from the jets finish it off.

On the TERRA HQ bridge, Haruka comments on how well Ayato has been doing - that he seems to have no doubts anymore. Kunagi comments that there isn't a person alive who has no doubts. Moving forward, we find Kunagi in his office in the dark, with Quon playing a violin piece for him.

The next day, Souichi arrives at the Commander's office to deliver his mail. He reports there is nothing going on and that he wishes these peaceful days could go on forever, as he looks at the Commander's blue bird (in cage). In his mail, the Commander notices a specific letter. He tells Souichi that he'll be gone for about 24 hours and that Souichi is in charge. Souichi asks him why he never gets a mate for his bird "friend" - that she looks lonely... before asking "She is a girl, isn't she?"

On the way out, Kunagi runs into Watari, who mentions that he was on his way to the planning session for the Mu War Memorial Service, which is apparently a sort of rememberance day for the events of the war. Watari comments that he doesn't mean to antagonize Kunagi by referring to the Memorial, saying he knows that today is a "special day" for Kunagi and that he should take it easy.

Ayato and Megumi are apparently about to go out to run errands. As they walk through TERRA HQ, they see Quon. When Ayato calls her name and she turns to say "Yes, Ollin?", Megumi asks "Ollin?". Ayato asks where Quon is going, and she replies that she "left something at Jin's." Megumi and Ayato don't know a Jin, wondering who that might be. On the bridge, the TERRA male crew are discussing what makes women happy. As Ayato and Megumi arrive, they ask Megumi what pleases girls to get - gifts like flowers and such. She replies in a joking manner "Sure, I'll have mine now.", but the bridge crew says she has Ayato for such things, to which she replies "Are you crazy? He puts soy sauce on his fried shrimp!" which of course starts the typical Megumi-Ayato banter. At this point, Isshiki walks in, chastising them for their childishness and wondering at the fact that these people are the first line of defense against the Mu. Souichi also arrives to explain that he'll be in charge as Commander Kunagi is out for the day. Isshiki walks off, commenting "I hope you won't make too many mistakes in the Commander's absence." The crew comments that it's an odd day, and Megumi follows this up by mentioning they ran into Quon, who had said she left something at "Jin's". The crew tries to think of who could be named Jin, when Kim
mentions that she is surprised that none of them know that Commander Kunagi's first name is Jin. As the crew reacts with shock to the fact that Quon is leaving things at "Jin's house", Ayato receives a call from Dr. Itsuki. Souichi mentions that Quon is often at the Commander's house late at night, a fact which makes the male bridge crew jealous. Itsuki asks Ayato to stop by his house, and Souichi asks Megumi to accompany him.

We flash to Quon, who is in the Commander's office and stops to look at the bird in the cage. Flashing back to the bridge, Kim is asking why Quon is always at the Commander's place, mentioning that Quon really isn't with TERRA or the military. Souichi mentions that Ayato is the same way, because he has a special ability to pilot the RX. He says that Quon is the same way, that she has some kind of special ability to help out.

Kunagi is at home, listening to a recording or phone call (it's not clear which at this point) of a young girl talking about her music and how much she misses Kunagi, and that she hopes he'll be at her next recital. At Itsuki's house, Megumi is looking at some flowers which have bloomed while Ayato listens to a recording of music that Quon has done recently. Apparently, the music caused the flowers to bloom in a different manner from the seed stock that they should have been. Itsuki mentions that he would have asked Quon about it, but he doesn't think she knows what she has caused to happen. Ayato reacts to the song he is listening to. He tells Itsuki that there's something not right about the song - that listening to it makes you sadder and sadder through its dissonance and discord.

Quon is playing her violin, and as we see her doing so, we flash to Kunagi, who is driving. He wanders around town, and we flash back to his office, where we see his bird is apparently wearing a ring on her foot. Kunagi has apparently run into Futagami in a watch/jewelry store. Kunagi buys a watch, and when Futagami asks the salesman to see the same watch, he is astounded by the price. Back at the house, Itsuki finds Quon crouching on the floor. She seems to be disturbed by the fact that she can't complete her music, saying something isn't right. He comments to her that Ayato said the same thing, to which she replies that Ayato understands because Quon and Ayato are alike, but then she wonders aloud "Will Jin be alright?"

Futagami thanks Kunagi for helping him find a stuffed animal toy for his niece. Kunagi turns to leave, but Futagami surprises him by saying "There's no need to be in a hurry, the ship won't be leaving port for a while." Futagami speaks to Kunagi about Watari attending the memorial planning service, then says they need to clear a few things up about the war. They talk about what happened when the Mu showed up - apparently American troops in Japan were said to fire first, leading to America's downfall in prestige. He says though that there were always rumored that the Americans were ordered to fire first, someone from the Japanese (I think) National Defense Force, and that this person dumped the blame on his subordinate,
which damaged that subordinate's career, and then vanished. This subordinate was also tricked or forced into using a tactical fusion bomb against the Mu, and it apparently led to the loss of a city. It is clear from the tone of the discussion and flashbacks that Kunagi was the subordinate under the military official who vanished, and that he didn't want to attack, but he was forced to do so by his superior. Futagami clearly knows this information, and asks why Kunagi is the commander of TERRA and not someone else. Kunagi surprises Futagami by mentioning that Futagami must have a connection to the Federation, causing Futagami to laugh about "being caught". Kunagi asks if Futagami can leave him alone, and as he walks off, Futagami mentions "Atonement for his sins..."

Back at Itsuki's, Quon leaves to go somewhere. On the streets of Nirai-Kinai, Ayato and Megumi (who is carrying some of the flowers seen at Itsuki's) run into Elvy and Haruka, who tease them about being on a date. Megumi mentions she got the flowers from Itsuki, insisting that they're not on a date. Megumi teases Haruka about having been out drinking, and they all tease Elvy about not drinking too much. She responds by grabbing Ayato's sleeve and saying "You're coming with me."

They go to a nearby arcade/bar. where Megumi reveals that she just learned Kunagi's first name is Jin, which Haruka seems to have already known. Megu mentions that they were talking about where the Commander might have gone, to which Haruka says that all she really needs to know is that it's a special day for the Commander. Megumi is upset that her sister "knows it all." Ayato and Elvy are dogfighting in an air combat game. Ayato is doing well, but Elvy eventually wins, shooting him down after distracting him with a compliment on his skills in the RX. As they leave, she asks him how long he intends to keep piloting.

As they (Ayato and Megumi) are walking home, Megu remembers that they forget to get a vase while in town for the flowers. Ayato asks her if she wants to go back, but she declines, saying instead that they should go look at the ships. In harbor is a restaurant cruise ship that Megumi mentions circles the island and is a hot date spot. Futagami comes across them (again, asking the humorous "On a date?" question) and points out Kunagi is getting on the ship. Megumi thinks that he must be on a date, and Futagami says she is sort of right - that the date is with his daughter - today is her birthday. Megu has an idea.

On the ship, Kunagi meets up with a woman who doesn't seem thrilled to see him. It's difficult to describe this scene without the reader seeing it, but apparently Kunagi was surprised the woman came, and they talk about how the girl in the video had a future. The girl in the video was Kunagi and the woman's daughter. Kunagi missed out on much of her childhood because of work, until she died in the war, presumably in the fusion bomb strike which Kunagi ordered. The woman mentions that she is leaving Japan, that she's changing her name, and that they likely won't see each other again - too many bad
memories. Before she leaves, she gives Kunagi an envelope with a piece of music, which is apparently the last page of a piece of music - the one Quon has been playing for him. Just then, a waiter arrives with the flowers Megu had, the stuffed squirrel Futagami had, and a note about how he should have a gift when meeting a girl. His ex-wife goes to leave, but he thanks her for coming.

Outside, Ayato wonders if they should have done anything, saying that sometimes family matters are something that outsiders can't understand. They head home.

Kunagi then heads to a graveyard, where Quon is waiting. Kunagi gives her the last sheet, asking her if she can play it for him. She's happy to do so for him, and she plays as he places the flowers on his daughter's grave, saying he knows that she is lonely, but she won't be much longer, but that he has things he must do. We notice the name Michiru on the grave, and at last we see that same name is on the ring on the bird's leg in his office.