The Anime's Ending
The last episode, "Na-Geanna", is much darker in tone and style than the rest of the series. It takes place on a Saint-Earth colony world, twenty years after Mahoro's death and the mutual defeat of Vesper and Management. Suguru "decided to never return to Japan, to that town where Mahoro no longer was," and is now a renegade half-cyborg hunter of the last "Management holdouts." He has only memories of Earth, and a sole companion who tries to kill Suguru for the bounty on his head.
As Suguru is either dying or badly injured, Mahoro reappears alive (which he greets with wry skepticism), asking to take him back to Hiryu "where everyone is waiting." The only explanation for Mahoro's reappearance is oblique: Matthew comments that she will leave behind on Earth a "memory of springtime" that has been disturbing her and will not be needed as Saint sets off to resume wandering the galaxy.
The story ends there, with no clear resolution even for the two main characters. With the exception of a cameo for Shikijo-sensei, the rest of the original characters' stories are left mostly or entirely unfinished.
The Manga's Ending
The manga ends similarly in theme to the anime, but the tone and style of the ending are far lighter and more consistent with the rest of the story. It takes place on Earth, twenty years after Mahoro's death and a decisive defeat of Management. Suguru has been working as a commander within Vesper, and has just returned to Earth from the final defeat of Management's last vestiges. As seen from his friends' perspectives (particularly Miyuki's), losing Mahoro has been tragic rather than degrading for Suguru.
Unbeknownst to Suguru, Mahoro was reborn as a baby shortly after her death as an android. She has grown up, and remembers Suguru. When he returns from Vesper headquarters expecting to find an empty house, she is there waiting for him.
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