(Act One)
The Milky Way stands before the Yamato.
Sanada reports on the casualties suffered during the recent battle, including Yuki's condition. Despite his best efforts, there's nothing Dr. Sado can do to save her with the resources aboard the Yamato. Sanada suggests placing her in the stasis chamber in the Auto-Navigation room. There, a shadowy figure (recognizably Mamoru) looks at the CRS core.
The Yamato temporarily regains comms with Earth, long enough to report they're on their way back with the CRS. Todo notices Okita is not on the bridge and is told about the captains worsening condition. Hijikata also notices Yuki is not there and is distraught to learn what happened to her. But the signal soon breaks up, much to Aihara's dismay.
While she's taking a break and drinking a cup of coffe in one of the observation decks, Niimi spots Mamoru's reflection in the window. She turns in shock but he's not there.
Yuki is placed in the Auto-Nav room. A sadened Kdai plays his harmonica for her, while Yurisha's flowers lie in a jar in the corner. The shadowy Mamoru spectre stands behind him.
Tokugawa visits Okita and the two goe on a stroll down memory lane. As Tokugawa leaves and goes down the stairs, Mamoru stands at the captain's door.
Despite his best efforts, Aihara can't get the comms signal back up. Kodai shows Shima a wedding invitation for none other than Kato and Makoto. While she's trying her wedding dress, Kato talks about how Kodai has been going around with a happy face, even though he's hurting inside.. Later, as she tends to the chambers systems, Makoto sees Yuki move inside the capsule.
Sanada and Niimi study how the CRS seems to be emmiting a strage energy pattern throughout the ship, resembling a brain network, as if the CRS and the Yamato are a living entity of some kind.They are called to the Auto-Nav room by Sado, as is Kodai. When he gets there, Yuki has just flatlined. Kodai is heartbroken but he asks those present - Sanada, Sado and Makoto - to keep Yuki's death a secret, in order to maintain the crew's morale, now that they're so close to the end. Above them, the CRS core glows eeriely.
(End of Act One)
(Act Two)
The wedding party. Kodai stands in the middle of the festive crowd and plays his part. Kato finally makes peace with Kodai and, much to Makoto's horror, hurges Kodai to keep the faith that Yuki will pull through (he doesn't know she's dead XD).
In the WMG chamber, turned into the CRS chamber, Sanada and Niimi discuss the true nature of the CRS and Mamoru's final fate. Kodai wonders the corridors, aimlessly, arriving at the Auto-Nav hatch. Inside, Mamoru, finally fully revealed, looks at Yuki. He turns as he hears Susumu entering the chamber. Kodai embraces the lifeless Yuki, remembering their history since they first met in the underground city, tears streaming down his face. Behind him, his big brother watches. Mamoru says something to Susumu and suddenly the CRS comes to life in a flash of light, shutting down afterwards. Sanada and Niimi observe the process, unable to intervene. The CRS is dead.
In the Auto-Nav chamber, Kodai is stunned when Yuki suddely opens her eyes and his tears of sadness are replaced with tears of endless joy. His embraces Yuki and the two finally kiss. Beside them, in the corner, Yurisha's flowers have fully bloomed.
Sanada and his team are incapable of rebooting the CRS. It's completelly dead. Sanada looks at the core and yells "Mamoru... No! Yamato... Is this what you wanted? What you wished for?"
The Yamato circles the Moon and Earth is now in sight, to everyone's joy. In his quarters, Okita ask Dr. Sado to give him a minute alone. As he leaves, Okita says "Sado-sensei... Thank you." Sado steps out, in tears. Holding his family photo, Okita looks up at the Earth and as tears stream down his face he hutters his final words: "The Earth... filled with my fond, old memories..."
The photo falls to the ground as Dr. Sado steps inside. He realizes what just happened and salutes the fallen warrior.
At that exact moment, the CRS reactivates, the core gleaming with energy, much to Sanada and Niimi's amazement. Niimi closes her eyes, bathed in the light and we hear Mamoru:"Goodbye, Sanada. Goodbye..., Kaoru."
Kodai enters the main bridge carrying a very much alive Yuki. Everyone is overjoyed and, following Yamamoto's lead, salute the young couple. Sado comes in but holds his tongue as to not spoil their mood, though he is happy to see Yuki's back. The Yamato flies to the night side of Earth, her engine glow fading in the Earth's shadow.
(Fade to Black)
Captions reading: "On December 8th, 2199, the Space Battleship Yamato returned to Earth".
The cast credits begin to roll. As they end faded clouds become visible as the camera pans up to reveal a blue horizon. The camera flies away from the Earth rotating to reveal a shining blue sphere glowing in the sunlight.
(End BGM. Fade to black.)