Disclaimer: I don't own RWBY.
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The epilogue would be a letter written by Jaune, to Pyrrha, on a Sunday some time later. Jaune reveals what's happened since the Affair.
Jaune and Ruby have moved out of the city and to a small settlement on the frontier, part of their efforts to rebuild their marriage. They have a new house, bought half with her money and pretty much all of his that he had from the old job. It's smaller than the one that Ruby bought in Vale- but he likes it more, less empty when she's gone even if the house is uncomfortably small when she's not. He has plans to expand it even if it means building the extensions himself- though he knows he won't have to work on it alone. The new home also has a garden he and Ruby and the children have all taken to mending together, complete with the new Family Roses at the heart. The new Rose Garden has no walls, not even a privacy hedge- but every neighbor who's come by and seen it has been impressed, and they're so far from the city that he can see the stars at night and the moon wherever it is in the sky.
Things aren't as luxurious as they were pre-Pyrrha, but they're healthier and Jaune is happier. Jaune now works for Schnee Dust Corporation on the frontier, helping build and expand new settlements and maintain the roads between them. Even if he could have gotten a better position through Ruby's connections with Weiss, this one is a modest entry position he could have gotten on his own, one with a sort of productivity and visible accomplishment that helps him feel like he's making a difference and not just a sinecure. He's also a part of the town militia to defend against the occasional Grimm attack- but considering that Ruby is a full-fledged Huntress in the local area, they're rarely needed. She lets him do it anyway, but in exchange he's given up drinking, just one of the compromises they've made since the Affair.
Ruby has adjusted to things as well. Team WBY never did find the person who sent the Dear Jaune letter- but Jaune will believe Ruby when she says that it wasn't Cardin Winchester. She's no longer the ambitious and far-traveling Huntress who spent months at a time traveling the world. She has fewer, shorter trips- and when she does, she makes a point of video chats frequently. No more weeks or months on end without hearing from her- and she's taken up where Pyrrha left off, training him along with their children, who are home-taught now that there's no combat school around. He'll never be good- never even as good as his kids- but it's brought the family together and allowed him to help the kids fight off a beowolf attack when Ruby wasn't there.
And speaking of children... things have been more up than down with them. The children, who he's supposed to call his flowers (or his Roses) rather than 'the children' as part of the post-affair changes, are relieved that their parents are back together, but still shaken by the fights and revelations. It's less about any stigma of being a donor baby, not at all that he's not 'really' their Father, and everything to do with realizing that he doubted them, and their feelings towards him, to the point of resentment and worse. Ruby being home more has helped temper them, but now they're over-compensating to even imagined slights against him… though to be fair he's probably doing the same in regards to them. Jaune is more than a bit ashamed that he projected his doubts and fears onto them, even though they were only guilty of being, well, imperfect children that he raised, and asks Pyrrha for advice and if she thinks they'd benefit from a different environment for awhile. Something to do over a summer while he and Ruby have their fifteenth anniversary honey moon? Ruby has promised to take him to see the stars from every continent, even the ones without Kingdoms. He also asks Pyrrha- knowing how hard this will be for her to hear him ask but there's no one he trusts more- for her advice on broaching the topic of Ruby having another child. One, or two, or more that he can raise without the doubt lingering over his head for years. He'd like a boy to call his own- to call 'Arc'- who could carry on the Arc family name, and one day be strong enough to protect Ruby when and where Jaune couldn't. If they do- if he does- when it comes time to train the boy, would Pyrrha be willing to even consider…?
The implications are that Pyrrha and Jaune have been maintaining a correspondence, with Ruby's knowledge. It's close, familiar- and it ends with fond musing of their briefly intimate friendship, and a wondering of how things might have been different if they'd met earlier in life. Jaune even reveals that, contrary to what Pyrrha told Ruby, he did try to initiate something sexual- twice. Once after Blake, and later after quitting the school and telling his children that he was going home. Both times it was Pyrrha who refused it, refused the him who she said wasn't being himself, and both times she talked him through his emotional state to the decisions of what they actually came to. He wonders where he'd be if she hadn't done that- if she'd simply given him what he thought he wanted, rather than the resolution she knew he needed- but he's never remembered her more fondly than the way she composed herself when he couldn't. He's grateful that she didn't let him live a life of regrets, which he would have carried with him had they eloped outright rather than tried to make resolution with Ruby. He knows that doing so ended up denying Pyrrha her chance… but he also knows he wouldn't have been able to commit himself to her as fully as she deserved had he still been haunted by lingering guilt and nibbling doubts.
Jaune closes that while he may wonder what life could have been had things gone differently, it's thanks to Pyrrha that he's resolved to make the most of the life he does have, to keep moving forward just like she told him in the kitchen so long ago. It's thanks to her that he's re-found happiness in his life- which is what he always wanted- and he truly wishes her the same for her. He encourages her in her pursuit, knowing that she won't quit looking for her own happiness or give up over him, because he has faith in her. In the new Rose Garden, he's carved out a single exception to Ruby's One Rule, finally managed to grow one flower that isn't a rose: a nasturtium. A flower as red as any rose but which means 'victory.' He includes one in the letter, which he signs 'Forever Yours, Jaune.'
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Fin
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Author Notes: Resolution- Jaune and Ruby are rebuilding their marriage and family, Jaune and Pyrrha remain friends (at a distance), and Jaune has found a sense of peace and happiness. This epilogue would have been posted the next Sunday of the finale, a week's pause to give time to catch breath and give a sense of the time passing.
The epilogue is a letter, rather than a direct encounter, to emphasize both the distance that has inevitably come between them since the reconciliation with Ruby- but that Pyrrha remains important to Jaune. Jaune writing his feelings into a letter is demonstrating Jaune finally overcoming his tendency to hide his feelings and how he's now able to express himself.
This is the end of the story, but tomorrow is my story analysis notes, themes and concepts... and a chance to answer any questions that remain.
Ask 'em while you got 'em.
