There have been multiple hints about the identity of Anakin Skywalker's real father in the prequels, and multiple theories about the origin of the Chosen One.
There are many theories and questions left unanswered in the Star Wars franchise, including the mystery of Anakin Skywalker's father. Most are irrelevant in the grand scheme of things, while others have a bigger impact on the Star Wars canon. The identity of Anakin Skywalker's father may never be revealed, but several interesting candidates exist.
There are hints and innuendos in the film as to who it might be, but no definitive answer. Some theories are stronger than others, based on the information provided by the film itself. With so much information on the Skywalker family and Star Wars in general, this isn't much of an issue in the actual movie. It does mean that there is still room for fans to speculate. With that in mind, here are some theories and how likely they are to be the true identity of Anakin Skywalker's father.
Someone From Tatooine
None of theories mentioned in the film, but it's still possible that someone from Tatooine was Anakin's father. Anakin's mother, Shmi, either forgot an old acquaintance, or chose to conceal who his father was. It's unclear why she lied because She said there was no dad. Choosing someone who doesn't have a father at all seems like an odd choice, considering how important this is to understanding Anakin.
In Star Wars Episode I - The Phantom Menace, Qui-Gon was skeptical of the Shmi Skywalker story and believed other things, but perhaps the Jedi Master was wrong. Shmi's claim that Anakin's father isn't human may be a mystery in the prequel trilogy, but it's not impossible. In the Star Wars universe, anything is possible.
Qui-Gon seems to suspect that the details of Anakin's parentage shared by Shmi indirectly fuel theory that the boy is a product of the Force. He believed that Anakin was the one who could balance the Force, and that he must have been created by the Force. Therefore, he is only able to have such a high midi-chlorian count as if he was originally created by them.
If this is indeed the correct answer, it is not clear whether it occurred naturally through the Force seeking balance, or whether the Australasia was manipulated by someone or something. All signs point to manipulation, but there are This is an opportunity for natural events caused by the Force's eternal journey to find true balance. Not the most compelling answer, but the one that makes the most sense. Qui-Gon seems to be one of the Jedi who knows the most about the Force, so if he thinks that's what happened, then there must be some truth to it.
One of the most popular theories is that Darth Sidious is Anakin's father. He could very well be his real biological father, which would explain their connection in some ways, but another explanation is a little more complicated. In this theory, the Force is still responsible, it's just different. The Force didn't create Anakin in a natural event until Sidious manipulated the Force to create a child inside Shmi. This would help fulfill Emperor Palpatine's ambition to fight a long war. He didn't come to power overnight. He waited and planned for decades to get to where he was during the events of the original trilogy.
This also adds more meaning to the scene between Palpatine and Anakin, where he narrates Darth Plaeg is wise. Palpatine talks about manipulating midi-chlorians to create life. On the surface, it points to Palpatine trying to bring Anakin to the dark side by suggesting that he will be able to save Padmé. However, it could also suggest that Darth Sidious himself manipulated the Force to create Anakin Skywalker, who subsequently set him on the path to becoming the great Sith Lord Darth Vader. This is the most likely origin story, as there are multiple hints in the movie to back it up, rather than pure speculation.
As far as theory goes, the idea that Qui-Gon Jinn was Anakin's father is probably the most outlandish. Qui-Gon found Anakin as a child on Tatooine, freed him from slavery, and set him on the path to becoming a Jedi. It's unlikely he's Anakin's father, as that doesn't have particular significance in the film, but that hasn't stopped fans from speculating for years. There is no definite answer, and such speculation is bound to occur. One theory that supports this viable option is that Shmi made up the orphan birth story to prevent Qui-Gon Jinn from being exiled And ostracized because the Jedi Order forbids love.
If the Jedi Council finds out, he will be expelled. The theory at the time was that Shmi decided to lie to protect Qui-Gon and Anakin. In a way, it's similar to Anakin's own love story with Padmé, who kept it hidden and ultimately led to Anakin's downfall and transformation into Darth Vader. There's an effective symmetry to this, like much of Star Wars canon in the Skywalker saga. In Anakin's case, it led to the birth of Luke and Leia, and in the case of Shmi and Qui-Gon, it led to the birth of Anakin. There's a viable way to turn it around so that theory fits the narrative, but it's a long way from being possible.
It is possible that none of theories listed above are correct, and the correct answer to Anakin Skywalker's father is another matter entirely. It's possible that this story could be told in a Jedi Legends-type project, but that's looking unlikely. Star Wars fans traditionally want to know every detail of every little character, so don't know such an important part The amount of information is overwhelming. While Darth Sidious may be the real answer, perhaps it's best to see it the way George Lucas intended. A mystery with no set answer, leaning toward the spiritualism of the Force, enhancing Anakin as a character in the process rather than knocking it down with a brilliant explanation.