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The Naboo Queen and handmaidens aren’t just a Queen and some girls that happen to look like her. That is the official story, but it isn’t true. They are a group of clones who take turns to wear the queenly regalia. If the one who’s currently Queen dies in public, it is explained that it was actually one of the handmaidens in disguise. The fact that handmaidens do that in dangerous situations is known, and smart enemies plan to take out the whole group at once, but it’s harder to do that, especially when they are never all together in one place.
The reason they rule young is because they are clones. They mature fast, but die young as well. Each Queen and handmaiden group will rule for a set time and then retire, well before the first signs of old age or organ failure can set in. Once retired, the former handmaidens can do whatever they please, so long as they either keep their deaths out of public knowledge or make sure there is a non-clone related explanation.
During the rule of Queen Amidala their planet is put in a difficult situation, and their attention is drawn to the galactic senate. Padme, Sabé and Rabé decide to become Senator Amidala together. It is harder, they can’t shadow each other around all the time. It is decided that one of them will play the senator, one her aid and one will be off duty and planet. The senator is supposedly the former queen, who kept one former handmaiden and close friend as an aid. They can’t be together all the time, and try to avoid having people think they ever take each other’s place. Of course they still do, but they don’t switch as often. And if the senator is killed she is killed. It isn’t really about keeping that kind of secret anymore. It’s more that they each wanted to take the job and were used to sharing a public persona and supporting each other. The one who is off duty at the time visits with the rest of the former handmaidens.
The Jedi know that they are different people, as they feel different in the force. But not that they are clones. When they know senator Amidala is going to interact with Jedi, they try to have Padme be her if she is available. Both because it makes it look like there is one senator who sometimes gets switched out for protection like before, rather than a shared role, and because Padme gets along with the Jedi best. Especially Anakin and Obi-Wan.
There is no romantic relationship between Padme and Anakin. She wouldn't do that without either retiring away from a shared role so that the secret could remain in her past, or telling him. She doesn’t want to do either. Besides, there is her early death and his position as a Jedi to keep in mind.
The former (and current, for that matter) handmaidens have a lot of thoughts about the clone army and how it is both different and similar to the work they were created to do. They work for the rights of clones. They consider going public with the secret, but it is an old secret that would affect many and that they could never take back. No single person has the right to make the call, and it is difficult to come to an agreement.
In the end, they sacrifice the secret that Naboo has kept for so long in order to make the galaxy listen and stop sending millions of clones to their deaths. However, they might imply that there was always one main Queen (or senator) with others ready to step in as backup. Possibly even that the rest are clones of that main one? Or maybe they give the whole story, to show how capable they all are. (They probably still make it out like there was only one senator, since it’s one thing to do something kind of iffy with the way you rule your own planet, and another to do so as a representative to the senate. Technically Naboo snuck in extra senators! Even if they never acted in the role at the same time.)
Important note: for this to actually work, Palpatine is either not a Sith or defeated. There is no order 66. He might or might not know about the handmaiden secret? Possibly he knew, but took it the wrong way and used it for inspiration to create the clone army. Yes, that sounds like him. And another reason for anger and angst and complicated feelings and the handmaidens hating on him specifically. Maybe he says something to them about it at one point, when they try to bring up their concerns with him, and that’s when they realise he is evil.
Anyway. They free the clone army! Yay! Also Palpy is killed or thrown in a deep force-blocking dungeon, and with him out of the picture the war comes to a close.
The clones are made citizens of the republic by way of Naboo. The way of the Naboo leadership is questioned. (Please note: the handmaidens may not have chosen to be created or their early training, but they did agree to step into the role. There are always at least a few who chose not to, and sometimes one will retire before the whole group/the Queen does.) It might still continue, now openly, or it might end in favor of some other system. No more clones are made for the army. Maybe Naboo stops making handmaidens as well. Hm. We’ll get back to that.
(But on that note: I’m note sure how the whole secret clones as Queen fits with Naboo’s passion for democracy. Maybe they elect other officials, just not the Queen? Maybe there was a vote on this system long ago and that vote is still holding the system in place? Maybe the people in the know vote on who should be made a clone template? I don’t know. It’s one of the bigger flaws with this idea.)
By this time, the Amidala clones are growing old. They have access to specialized medical care and the end won’t be nearly as rapid as for the Fett clones in the army, but they will still die.
Maybe Anakin and Padme do enter a romantic relationship after all. The handmaiden secret is out and the war is mostly over, so Anakin (inspired by the honesty of the handmaidens) decides to retire from the Order and live with Padme on Naboo. Senator Amidala has retired so the three of them can grow old on their home planet, the one they were once created to serve and protect and rule, with the rest of their handmaiden sisters.
Padme tells Anakin that she is going to die of old age soon, but of course that just inspires him to want to spend every last second with her. They end up getting married. It’s a big deal, front page across the galaxy. Obi-Wan is the space equivalent of best man. All of the Amidala handmaidens (minus Padme herself) are maids of honor. Asoka is ring barer. Shmi is totally alive and free and attends the wedding, along with her husband and stepson.
And then Padme gets pregnant. It was an accident, and it creates a problem. Especially since she is already old and growing weaker all the time. There is a serious discussion about the possibility of abortion, and no one dismisses it, but in the end Padme decides that she wants to go through with it. This may be partly for not entirely healthy reasons, like wanting Anakin to have a piece of her left once she is gone. But she always wanted a child. She gave up on the idea when she chose to become senator Amidala, and was never serious about becoming a mother before then, but now that the chance has presented itself she doesn’t want to let it go.
Anakin is partly happy, partly terrified. But he has a support system and no Sith whispering in his ear, so he can totally do this. He’s less sure he can do it when they find out Padme is having twins. Twins! In an already high risk pregnancy!
But they have access to the best medical care in the galaxy. And there are no Sith choking Padme. So she lives! Yay!
Sadly she does still die later, because for all that this has some fix-its it’s still also very much a tragedy. But she gets to see the first two or three years of the twins' lives. Just enough for them to remember her later, especially since they are force sensitive. And she records a lot of holovids for them to watch as they grow older.
The galaxy mourns Padme’s death. She was neither the first nor the last Amidala clone to pass away, but she was the one most publicly known. She is buried next to the fellow handmaidens who went before her.
Anakin falls apart. But does not Fall to the dark side. He has the twins to care for, and is surrounded by a robust support system. Obi-Wan is still in the Order but not on the Council, and took a sabbatical on Naboo when Padme’s health started to really go down-hill. Ahsoka also comes to stay, along with her padawan (I have no idea who said padawan is, but Ahsoka is totally great with them and also a member of the surviving and improved Jedi Order). The living handmaidens and their families are there. Probably Shmi and the Lars family. Lots of friends. Clones! So many clone brothers. Anakin still loses his wife and the love of his life, but he is never alone.
Luke ends up becoming a Jedi - at an older age than normal - and Obi-Wan is his master. Leia becomes the democratically elected, non-clone Queen of Naboo. She isn’t the only one. When Naboo stopped using cloned handmaidens, they kept having groups of young women sharing the role. It isn’t a secret anymore, but still spreads out the responsibility on multiple people and allows them to keep the old traditions in a new way. And while they are still young they are less young than the cloned handmaidens were.
Luke and Leia are children of a clone, and they do inherit some health issues, but nothing too terrible. Especially since they are both strong in the force.
And one day Anakin and Obi-Wan are having tea on Naboo and talking about old memories. Qui-Gon comes up, and the prophecy he believed in. And Anakin says that chosen one or not, Padme was the one who really brought balance and peace. Her, and the other handmaidens, and Luke and Leia. And Obi-Wan looks at Anakin and says ”You brought peace and balance to the force within yourself. You used to feel like a storm, but now you are the greatest sense of calm and light, happiness and love that I have ever felt in the force. I cannot say if that is what the prophecy meant, but it is enough for me.” And this Obi-Wan, who has lived without war for so long, who has seen Anakin grow and bloom outside the order, and who has helped reform said order, this Obi-Wan can go on to talk about his feelings without there being some sort of emergency spurring him on. Can talk about how much he loves Anakin, without having to hold anything back. Their friendship is strong and bright and beautiful, and it doesn’t hurt either of them.
And the clones. The former army. They can’t be forgotten in a story that is so much about them. They also still die of clone related reasons, and that is still a tragedy, but they get to live first. Live freely, without war and orders. Many of them settle down on Naboo. Others go to other planets, or live on various spaceships. Many dedicate themselves to freeing slaves across the galaxy. Fives becomes the first clone to act as a senator, excluding the Padme/Sabé/Rabé trio. The clones find various jobs and hobbies and things to enjoy. Friends and family, not just among themselves and the Jedi, but other people as well. First mainly on Naboo and Mandalore, but soon enough in all kinds of places.
They still die, yes. And with no more clones being produced that is the end of their story. But they had so many different stories, so many lives, and they are not forgotten.
Hundreds of years from now, younglings will learn about this in their history classes. And when they learn about Anakin Skywalker, they won’t know about any prophecy. He will be known as the husband of Handmaiden Padme Amidala, who changed history. As a Jedi general who has once worked with the famous Captain Rex. The father of Queen Leia, one of the best loved rulers of Naboo during the first generations in the new system.
Obi-Wan, Ahsoka and Luke mostly faded away from the common history. There are still footnotes about them, but not much more. If you were to look through the Jedi archives you would find a different story, but still not one that was overly focused on them as individuals rather than what they did. Jedi move through history, and they bring about many big changes, but they are rarely talked about afterwards. That tends to be the way they like it.
There is no reason for any of the Jedi, current or former, to stick around as force ghosts in this story. They join with the force, and they are content. The only ghost still around is Qui-Gon Jinn, who became one when the galaxy was still in such turmoil. He might still be able to join with the force, and one day he will try, but he’s not in any hurry. There are still many things to see, even when he can’t interact with them. He spends most of his time on Naboo, the blue green planet where he had once been killed, and where so much of history had been rewritten.
He stands, as an invisible spirit, on the shore of a lake. A group of young women, newly elected queens, are getting ready for a diplomatic visit to their Gungan neighbours. The queens look nothing alike, no make-up in the world could make them pass as one another, but they are all smiling the same bright smiles and their eyes are glittering with hope for the future.