In Episode 1: The Phantom Menace, Anakin's mother, Shmi, said that he does not have a father, although it seemed to me that she doubted that.
Is there a canonical answer as to who Anakin's father is? If so, who?
According to Wookiepedia, Anakin didn't have a father. While "virgin births" can and do happen in real life among many non-mammalian life-forms, all of them are daughters and are effectively clones of the mother (or twin sisters if you prefer).
Skywalker's mother, Shmi Skywalker, claimed that her son was conceived without a father, but could not explain how that had happened. It was the theory of Jedi Master Qui-Gon Jinn that the will of the Force caused his birth. There is evidence to suggest that Skywalker's birth may have been engineered by the Sith Lord Darth Plagueis as part of an experiment in immortality.
And pursuant to rule 34:
If you are old enough, check out the March 1985 issue of Penthouse . Males under about 30 cannot tell them apart, while females of all ages surveyed can distinguish mother from daughter.
In addition, although Darth Plagueis did attempt to influence the midichlorians to create the ultimate Sith weapon alongside Darth Sidious, the experiment was ultimately a failure, and the midichlorians, sensing the Sith's inherent malevolent intention, not only refused to do so, but in retaliation, conceived Anakin Skywalker in order to destroy the Sith once and for all.
So, according to this, neither Darth Plagueis nor Darth Sidious are Anakin Skywalker's father, the midichlorians really conceived him without any outside direct intervention.
Shmi specifically states there is no father. By later conversations among the Jedi, it is generally to be concluded that the midichlorians created Anakin in Shmi to bring balance back to the force.
She never claimed to be a virgin when he was conceived, so it is not necessary to assume it was a virgin birth, just that there was never a biological father.
When writing The Phantom Menace, an answer was actually never planned by George Lucas, as it is simply echoing the story of Jesus Christ.
But in the first draft of Revenge of the Sith, when Palpatine tries to lure Anakin to the Dark Side and the young Jedi finds out that Palpatine is actually a Sith Lord, Palpatine tells him that he was the one who orchestrated the death of his mom.
In that same script, there is no mention of Darth Plageuis, but Palpatine tells Anakin that he fathered him through midichlorians in his mom.
The canon "answer" is that the Force itself caused Anakin to be conceived w/o explanation as to the biophysics involved. IMO, this has been ASSUMED since Shmi simply declares in Episode I that Anakin had no father, that she'd become pregnant w/o benefit of intercourse (poor Shmi, for all that grief and work she deserved at least one night of fun). This echoes the 'miraculous' conception of Jesus Christ. Likewise, following the script of Episode I doesn't preclude a biological father for Anakin, but also gives no clues as to the identity of said father.
In the first movie Phantom Menace, when Anakin Skywalker is a boy, his mother said that he has no father. I was thinking Darth Maul — could Darth Maul be Anakin's father? It seems that when Anakin becomes a Sith as Darth Vader, his son Luke fights him. Maybe the father and son fight or sense one another in these films? Maybe Anakin's mother knew about Anakin's father turning to the dark side and becoming that Sith in the first movie.
There was a line in The Phantom Menace that was cut out of the original script in the scene where Qui-Gon Jinn and Shmi Skywalker are talking about Anakin's father that I personally found interesting:
SHMI: There was no father, that I know of... I carried him, I gave birth....I can't explain what happened.
This tells us that when Anakin was born, Shmi wasn't in a current relationship. By this statement, it could seem possible that Anakin could have had an actual father (but the line was cut out of the film). Therefore, the correct answer to the question would be the Force, since it is canon.
If Anakin had a human father -- which, as pointed out, is unclear -- the best candidate is probably Count Dooku. Note that the fights between Anakin and Dooku in the second and third films of the prequel resemble the fights between Luke and Anakin in the second and third films of the original: the younger Jedi loses a hand in the second film duels, but turns the table in the third film and defeats the Sith in the third film, cutting off a hand -- and then is egged on by Palpatine to kill his defeated opponent. The differences are that Anakin cut off both of Dooku's hands and then killed his defenceless opponent, while Luke cut off only one of his father's hands (apparently the replacement for the one Dooku sliced off) and refused to kill the not-yet-helpless Vader.
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