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The Anakin/Padme romance was a Jedi Mind Trick by Palpatine.
Anakin and Padme, despite their interactions in Episode I, didn't have much in common. Anakin was a totalitarian, desperate for stability in his life; Padme believed in democracy, however inefficient. Anakin was from Tattooine, a culture that emphasized practicality; Padme was from Naboo, a culture that loved beauty. Anakin's from a warm planet; Padme's from a cool one. There's no reason for them to get together. The only thing it does is serve Palpatine's plan — so what do you know? Palpatine mind-tricked them both to fall in love, knowing it would draw Anakin to the Dark Side.

Being Padme's bodyguard is a high-risk job.
Sabé, Padme's decoy in the first movie, is not around and has been replaced. What could have happened to her? Maybe this wasn't the first assassination attempt on Padme. Maybe it's even more dangerous to be Queen — hence why as a Senator, Padme doesn't get a formal decoy. Or maybe Sabé had the same thing happen to her in-universe as out — she grew five inches taller than Padme and would no longer be a convincing double, so was pensioned off to a career elsewhere.

"Deathsticks" aren't thinly veiled cigarettes — they're stronger narcotics.
They might be ancient talismans that, when burned, give the user certain powers, like you see in certain anime. They're probably visual powers — hallucinogens of some kind. Wookieepedia seems to think so. And you wouldn't have ordinary cigarettes sold in a bar by someone who looks like a weak-minded druggie. The Jedi are trying to eradicate them because they want a monopoly on mystical vision powers.

Clonetroopers are genetically engineered to be gay.
How else are you going to deal with thousands of young human males, accelerated through puberty, without any females around them? You get them interested in each other. It also prevents the spread and dilution of the Kamino biotech, and explains the many Trooper discos and male-only bathhouses in LEGO Star Wars. Sure, it doesn't work every time (look at Darman and Jangotat), but it works often enough to make an army. And it's more reliable than trying to eradicate their sexual instinct entirely. And it worked for the Spartans.

Jango Fett missed when he shot Zam Wessel.
He was aiming for Obi-Wan, but he hit his partner by mistake. He panicked, didn't try another shot, and flew off. It makes perfect sense when you remember that he's the template for all those Stormtroopers.

Palpatine arranged to have Anakin's mother killed.
It would have been pretty easy for him to bribe, force, or otherwise convince the Sand People to attack a specific moisture farm.

Anakin went to kill Watto right after killing the Sand People.
It was always his plan in coming to Tattooine — he would free his mother and kill the one who enslaved her (even if he was better than most slave owners). He went into a murderous rage upon finding out what happened to his mother, but that doesn't jive with his oddly forgiving attitude toward Watto when they interact on screen. He knew what he had to do; he internalized his anger at Watto and went after his mother first. Then he went back to finish the job.

Anakin actually considered working for Watto as a debt collector.

While on Tatooine with Padme, Anakin took time to grieve his mother and give thought to his future. Padme had already said she wasn't interested in a relationship with him. Even so, Anakin was ready to do anything to win her over, despite not knowing if he and Padme would be able to make a life together. For all he knew at that moment, he would have to leave the Jedi Order, and there was no guarantee her rich family on Naboo would accept him, being a person of lower status. They might disinherit her if she married him. Moreover, Padme's tenure as a Senator wasn't set in stone. If she lost the vote, he might have to support both of them eventually. Watto mentioned before that he could use someone with Jedi skills for repo jobs. He also had family on Tatooine now—sort of. So even though he hated sand and his former owner, Anakin would have been willing to work for Watto as hired muscle in order to be with the woman he loved.

Anakin has Stockholm Syndrome for Watto.
As an alternative to the above WMG, Anakin feels sympathy for Watto despite how he treated him and his mother. Anakin never uses his opportunity as a Jedi to bully him. He treats him pretty respectfully in Attack of the Clones, even as Watto admits he sold his mother to some stranger. Consider that Watto treated Anakin and Shmi better than most slave owners, and there were characters like Jabba the Hutt to worry about; Anakin may even consider Watto something of a father figure.

Captain Typho has seen the Silence.
His eyepatch looks suspiciously like one of the eye drives used to counteract the memory effects of contact with them.

Jango had good reason for hiring Zam and choosing bugs as the means of assassination.
He was attempting to cover his own ass by keeping as much distance from the job as possible, in case it caught up with him. He does have a kid to raise, after all.

Padme isn't a fool who believes Anakin is a good guy despite his fascist leanings and mass murder. She just overlooks it because he's hot.
At several points, Padme seems impatient with Anakin — for example, her chilly reaction to his interrupting her when she's speaking to the new queen. She emphasizes a lot that he's still a padawan. She seems to disdain his total lack of understanding of politics, and she doesn't understand his life as a Jedi or his violent tendencies. But he's hawt, and she wants a piece of that action.

This explains why she dresses provocatively and talks sex a lot, and in the same breath tells Anakin they can't be together. She's just looking for a one-night stand. Anakin is kind of obsessed with her and wants a long-term relationship. She thinks she's not getting through to him and asks him about Jedi law on "love", probing whether there's room for casual sex. She goes on her unplanned vacation to Naboo hoping to explore a side of life she's never found time for before, and she's trying to tell Anakin that she's after a quick fling; when she tells him it's impossible for them be together, she means long-term. (This, by the way, is how Natalie Portman saw it in the DVD featurette).

Padme didn't react much to Anakin killing Sand People because she's got some Fantastic Racism herself.
It ties into an Episode I WMG that most people on Naboo are racist against non-humans. Look at their relationship with the Gungans, and the extreme mistrust the Gungans hold toward the Naboo. Look also at Naboo native Palpatine being the guy who started the Empire. Padme is a cultured Senator and perhaps more tolerant than Palpatine, but she still finds it real difficult to feel sympathy for the Sand People.

Lucas went through a divorce so nasty that Indiana Jones and the Temple of Doom had a guy get his heart ripped out. He hadn't been dating for years by the time he made Attack of the Clones. He may be capable of writing a love story in principle, but certainly not in the mindset he was in when he made this particular film.

Padme never loved Anakin.
It was all the Jedi Mind Trick. It's pretty awful. It may even have been subconscious.

Darth Maul ordered the Clone Army's creation.
Darth Maul was alive at the time the army was said to have been commissioned. He was working for Palpatine. Darth Maul was the guy. He probably was the guy who killed Sifo-Dyas, and used his name to place the order after he died. Alternatively, he was Sifo-Dyas, a Jedi who faked his death, turned to evil, and adopted the Sith title "Darth Maul".
  • Jossed.

Jedi!Anakin was written as a parody of Star Wars fandom.
Much like the Abzorbaloff for Doctor Who, or Superboy Prime for DC Comics, Anakin in Episodes II and III was written to make fun of some of George Lucas' more passionate "fans". Just imagine Anakin saying "George Lucas raped my childhood!" and it makes perfect sense.

Clone Troopers aren't cloned from Force sensitives for pragmatic reasons.
It has nothing to do with the possibility of going crazy from sharing the same Force powers. Palpatine could have easily made, say, Sifo-Dyas the template. There are two good reasons to choose a Badass Normal: First, he avoid the awkward questions about the army's template when he claims the Jedi are trying to take over, and second, it would be easier for him to control the army.

Dooku's allies' motives for joining him:
  • Geonosis: They are in a losing battle with another species. The Republic supports the enemy, so they're with the Separatists. The fact they are trying to develop the Death Star either shows that either they're desperate to win the war, or hate the enemy so much they want to blow their planet up. They trust Dooku enough to share the weapon with him.
  • Muun: They want to profit off this war. Also, they may have Trade Federation ties, and a Separatist Galaxy would be more tolerant of their more dubious money-making ventures.
    • Before Palpy disposed of him, Darth Plagueis may have had something to do with this, too, being a Muun businessman and all.
  • Skakao: They get to prove their technological prowess with battle droids, and the Republic greatly restricts the crazier tech they're good at.

The Jedi's ultimate goal is the extinction of all Force sensitive people.
Episode I shows that Force sensitivity has a biological component, while Episode II confirms that Jedi are not allowed to get married and have children. This means that the Jedi are selecting against Force sensitivity. As for why, there are a couple of reasons:
  • Control. According to supplemental material, there are a few thousand Jedi and a few million habitable worlds in the Galaxy. It's already a huge challenge for the Jedi to police and defend the entire Republic — imagine if half the population was Force sensitive.
  • Religion. The Old Republic Jedi seemed rather staunchly dogmatic. They may believe that the number of Jedi can only properly be decided by their Sentient Cosmic Force, not by such things as natural selection or a Super Breeding Program. To this end, they prefer Force sensitives to appear randomly, as this will give them insight into the will of the Force.

Kaminoans are not native to Kamino.
It's covered completely in an ocean, and it isn't a planet where the race we see would naturally develop. Kaminoans come from another world in their solar system, which was rendered uninhabitable in a cataclysm. This happened before they possessed hyper-drive, so they could only colonize the water world of Kamino.

It's an alternative to the Star Wars Legends continuity, where they are native but suffered a devastating planet-wide flood and had to recolonize.

The "thousand year" contradiction is a deliberate Retcon.
In A New Hope, Obi-Wan describes the Jedi as having defended the Republic for a thousand generations, whereas in Attack of the Clones, we hear them say that the Republic has been around for only a thousand years. George Lucas realized how ridiculous the "thousand generations" sounded and tried to change it without anyone noticing.

Sifo-Dyas is an Aborted Arc.
It looks like a cipher name, something George Lucas has never been very good at disguising. Indeed, the story of the name comes from someone misspelling "Sidious" — "D" and "F" are next to each other on the keyboard — and Lucas liked how the name looked. Originally, the plan was for the Jedi Master who commissioned the clone army to be a disguised Sidious, but Lucas dropped that. Maybe he was planning to change it to something more elaborate, leading to The Reveal that the Jedi had a traitor in their ranks. When Lucas realized how obvious the cipher would be, he scrapped that and created Count Dooku instead to fill in the "Jedi traitor" role.

Dooku seduced Jocasta Nu to gain access to the Jedi archives.
In a deleted scene, Jocasta muses over Dooku with some fondness while telling Obi-Wan of "the lost twenty" Jedi. It's possible that she had a thing for Dooku, and he used it to trick her into granting him access ("Say, how does that work?") so he could delete the data about Kamino.

Cloning Force sensitives is extremely difficult, if not impossible, in the new canon.
The Emperor never made a clone army from Darth Maul, or Anakin, or anyone else powerful enough that he could get away with being Obviously Evil. The Kamino cloning science is purely scientific, so their knowledge of the Force is limited. The Force wouldn't like it if its power were forcibly replicated, so it's impossible to do it without using the Dark Side, and even then it's still really hard. If, say, Palpatine cloned himself in the new canon, at best it would yield a clone with no connection to the Force. This is one major reason why Palpatine cloned a Badass Normal, the other being subtlety.

Technically Jossed by The Rise of Skywalker, which shows that Palpatine successfully made a Force-sensitive clone of himself. But since that clone was the first successful attempt after at least one failed one, was clearly in poor health, and otherwise looked really freaky, one can still conclude that it's really difficult to make a Force-sensitive clone, and practically impossible to make enough for a clone army.

Sidious kept Shmi in slavery.
The Jedi are totally incapable of freeing Shmi, even after they escape with Anakin. They don't bust in guns blazing. They don't just buy her back. They don't even make sure she doesn't get sold somewhere they can't see. Something was blocking them, and that was Sidious's machinations behind the scenes.

Obviously, Sidious did this to ensure that Anakin would be as troubled and emotionally vulnerable as possible, so that he could be manipulated into Darth Vader. Sidious (as Palpatine) surreptitiously used his power — both with the Force and the bureaucrats — to ensure that no one could free her, either by tying up the funds, filibustering, or preventing everyone involved from personally travelling to Tatooine. It would be easy for Palpatine to find a crisis somewhere to distract the Senate, or claim security reasons (probably legitimate) to block traffic to Tatooine.

The Imperial March was playing in-universe during the military parade
The actual Imperial March actually exists in-universe as "the martial theme of the Imperial Navy" and is a somewhat popular music (to the point it's used as an elevator music, and it's hummed by Separatist battle droids) and, in Legends, it was chronologically first heard over three thousand and half years before the movies. Given it apparently started out as a Republic military march, an actual military parade would have been the perfect moment to play it.

Count Dooku legitimately considered turning Obi-Wan to his side.
It's in the nature of Sith apprentices to overthrow their master, and Dooku was a lot more idealistic than Palpatine. Some of Dooku's actions imply that rather than antagonize the Jedi, he'd prefer to convince them to help or stand down. Reaching out to Obi-Wan was a Xanatos Gambit; either Obi-Wan rejects the offer and the Reverse Psychology serves his and Sidious' agenda, or he accepts and gives Dooku a powerful ally. Dooku can sell Sidious on this as a way to turn Anakin to the Dark Side (or at least obstruct the Jedi politically), but his real motivation would be to overthrow Sidious (or at least retain that option for when Sidious goes too far).

One way to think of this is that while Dooku adopted Sith philosophy, he never really wanted to abandon his former Jedi comrades. He still respected them as people (or other life-forms) and their skill with the Force. He may have been particularly close to Qui-Gon and motivated by revenge against Sidious for ensuring his death; Obi-Wan being Qui-Gon's apprentice, Dooku would see him as similarly motivated.

Ultimately, Dooku gave up on the plan once Obi-Wan proved to be incorruptible and begrudgingly abandoned any plan to outgambit Sidious, hoping instead to fly Beneath Suspicion. Sidious sniffed out anyway that Dooku's loyalty was in question, which further motivated his order to eliminate Asajj Ventress in Star Wars: The Clone Wars — he wanted to do it before Dooku and Obi-Wan had the opportunity.

Qui-Gon would have joined Dooku, but they wouldn't be working for Sidious.

Both Dooku and Qui-Gon were strong with the Force, and both believed that the Jedi Order's focus was too narrow and political. They would have started their own Force tradition centered around Anakin's identity as the Chosen One. Their shared ideals would have dissuaded them from embracing the dark side, but their creed would have been more lenient than the Jedi in some ways, such as allowing marriage for members (Anakin may have been able to marry Padme openly if he had been Qui-Gon's ward in this new order.)

"Deathsticks" actually kill you.
Of course, we all remember the scene where Obi-Wan Kenobi is confronted in a bar by a drug dealer who tries to sell him "death sticks". It's a funny scene, and doesn't seem confusing at first, but when you more closely examine it, you realize how absurd it is that this drug dealer (Elan Sleazebaggano) is trying to sell his death sticks to Obi-Wan, who is clearly a Jedi. So, what if "death sticks" aren't really drugs, but a type of poison that is actually fatal? Perhaps Sleazebaggano isn't really a drug dealer, but is working for an organization (possibly the Hutts) who are using the death sticks as a covert way to kill people they want out of the way? After all, it seems like a classic "gangster" thing to do, and the Hutts probably have plenty of reasons to want a Jedi like Obi-Wan out of the way.

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