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When you watch Star Wars: Revenge of the Sith, does anyone else find it curious that no one around Padmé Amidala (in the story, anyway) seemed to wonder who fathered her child? Her marriage to Anakin Skywalker was a huge secret, after all, so he shouldn't have been a likely candidate in most of the Galaxy's minds. As it so often does, Star Wars: The Clone Wars makes everything in Star Wars richer and deeper, and I think it gave us the answer. After going through a rewatch of Star Wars: The Clone Wars, reading some other material, investigating the timeline, and doing some back-of-the-envelope calculations, I think I've got the only solution:
Everyone assumed Rush Clovis was the father.
"Who?" you're asking. I'll grant that Rush Clovis isn't a household name, but in Padmé's social circles he was. And it couldn't be more obvious when you look at all the available data.
In order to understand all of the context, we need to go back to the Season 2 episode of The Clone Wars "Senate Spy."
In this episode, we learn about Padmé's previous relationship with Clovis, a former Republic Senator hailing from the Scipio system. Clovis is an old flame of Padmé's, and Anakin was shocked to learn that Padmé and Clovis had been in a relationship together before their marriage. When Clovis is suspected of spying for the Separatists and Padmé volunteers to reignite sparks with her former lover in order to catch him in the act, let's say Anakin wasn't exactly thrilled about that. But since the Jedi and the Senate leadership all knew about Padmé's prior relationship with Clovis, they all think she's a natural fit for the mission. It was common knowledge.
But this episode ends with the Separatists trying to poison Padmé in a bid to keep their dealings secret. Clovis, for his part, tries to help, but he is indeed exposed as a spy. Anakin is completely unsympathetic and leaves Clovis to suffer the consequences after rescuing Padmé.
Time heals the rift between Anakin and Padmé and the war keeps them distracted, but in the days after Ahsoka Tano's departure from the Jedi, Clovis arrives back on the scene.
Padmé is sent to deal with the Banking Clan on Scipio to secure better terms on loans for the Republic. Clovis is assigned to her, but she refuses to deal with him. He finally convinces her that he's on her side when he brings her into his plot to bring down the corrupt Banking Clan.
Though he sets off Anakin's jealousy and takes a beating for it, Clovis and Padmé work well together until Count Dooku blackmails the reformed senator.
Through the ordeal, after rekindling Padmé's trust, Clovis is killed, a disgraced hero.
He's gone. Just like that.
After Anakin's jealous outburst, Padmé doesn't seem to think it's a good idea for them to see each other for a while. Anakin goes off to fight in the war and they barely see each other for a brief time. But a crisis soon brings them both to Batuu. Yes, that Batuu. In Timothy Zahn's Thrawn: Alliances, Anakin and Padmé both end up at Black Spire Outpost, chasing the mystery of a murdered handmaiden. After they foil yet another Separatist plot, they finally get some alone time, heading back to the galaxy from Batuu.
Anakin and Padmé are forced to go their separate ways. Anakin is assigned to the Outer Rim sieges (which we're currently enjoying in the first arc of the final season of The Clone Wars), and Padmé resumes her work in the senate.
They don't see each other again in person until she reveals her pregnancy to him on Coruscant. (Yes, that means that it seems that Luke and Leia Skywalker were probably conceived on the way back from Disneyland.)
As Padmé grows more and more visibly pregnant, why did no one wonder who the father was?
Rush Clovis is really the only possible answer.
The timeline matches up pretty well, and their prior relationship was common knowledge. Who would have blamed Padmé for reigniting that old flame while dealing with the crisis with the banks? But he's dead now. Why bring it up with her if it's going to cause nothing but heartache for her if you're right and embarrassment for her if you're wrong? And isn't that a very personal question? Obi-Wan asking in Revenge of the Sith is only a formality. He knows it's Anakin, and the events in this week's episode of The Clone Wars, "A Distant Echo," prove it.
And I think Padmé is savvy enough of a political operator to let people think that Clovis could have been the person who fathered the child, if only to avert suspicion from her relationship with Anakin. But I doubt she'd do that if Anakin were around. I can't imagine Anakin would want to listen to people assuming that his children were fathered by a person who made him impossibly jealous.
Human relationships are complicated.
So is the palace intrigue of being in a secret marriage with a Jedi.
But I think that's the answer to the question. When people wondered who the father might be, Rush Clovis was the easiest answer at hand. When the story about her death circulated and that the children had died also, no one ever gave it a second thought.
Except for perhaps the Naberries. I'm still wondering what they thought about everything that happened to their daughter. They're still out there. Perhaps one day we'll find out.