So where were we? Ah, yes. 'Attack of the Clones'. The one title that everyone really hates. Everyone wanted this one to be called 'The Clone Wars', but it doesn't really sound as "Saturday morning serial" as the other five films. Even so, it's a title that doesn't suck, which puts it head and shoulders above the one Lucas used.
We pick up the action a few years after the events of 'The Phantom Menace', on Coruscant. Queen Amidala has come to the Republic's heart to try to find some way out of what seems to be a brewing civil war; although their attempt to seize Naboo failed, the Trade Federation continues to foment unrest throughout the Republic. Although the Queen doesn't want to see chaos spread, she also believes that Chancellor Palpatine's heavy-handed methods are making the situation worse. She's hoping to speak privately to him, and convince him to find common cause with the Separatists.
Her attempt fails almost before it's begun, as her ship is destroyed by a Separatist bomb just moments after she leaves it. Even here, on the Republic homeworld, Separatist threats lurk. The Jedi assign her two old friends to protect her, Obi-Wan Kenobi and his padawan, Anakin Skywalker, both recently returned from an extended peacekeeping mission on the Outer Rim of the galaxy. But Amidala is shocked to find that during the period she's been separated from her friends, Obi-Wan's relationship with Anakin has deteriorated. Obi-Wan is scarcely older than his student, and Anakin has proved to be powerful in the ways of the Force. Anakin challenges his mentor's every decision, and Obi-Wan over-exerts his authority in an attempt to get his student to listen. And far from smoothing things over, Amidala's return makes things worse...Anakin seems to remember all too well that he had a friendly rivalry with Obi-Wan over her affections.
Despite this, the two work together elegantly to stop another attack on her life, this one from an assassin equipped with strange weaponry. He fails in the attempt, but ominously, he manages to hold off two well-trained Jedi and make his escape using a jetpack device unknown to the Republic before now. This new development prompts Chancellor Palpatine to postpone his meeting with the Queen; two attempts on her life in as many days makes it clear that Coruscant is not safe for her. He confers with the Jedi Council, and they agree to send Amidala into hiding, with Anakin as her bodyguard, while Obi-Wan (as the more experienced of the two) tracks down these killers and ensures the Queen's safety on a more permanent level.
Obi-Wan takes the clues (a tiny dart left by the mysterious assailant, and his description of the attacker) to the Jedi Archives, but finds nothing. To all the recorded histories of the Jedi, it is as if the attacker never existed. Frustrated, he turns to the Jedi Spirit Halls, where the Jedi whose physical forms have died rest in spiritual form, dispensing advice to the living Jedi. Sure enough, his old mentor, Qui-Gon Jinn, recognizes the dart as an artifact of the legendary Mandalorian technocrats, a species from the Outer Rim who are experts in every kind of science. But Qui-Gon is puzzled...the Mandalorians have been reclusive for some time, but the Archive should have records of them. It doesn't seem possible, but the Jedi Archives might have been tampered with. This revelation unsettles Obi-Wan more than any mystery assassin could as he sets off for Mandalor.
Meanwhile, Anakin takes Amidala off to the more obscure parts of the Republic. But the assassin follows them everywhere--Anakin does battle with him on the forest world of Yavin, and finds that this mysterious "Boba Fett" is the equal of a Jedi in combat. Anakin hadn't even imagined this to be possible; the Jedi are supposed to be warriors without compare, the elite defence forces of the Republic. A lone Jedi is as great a threat as a company of soldiers...but Boba Fett is as great a threat as a Jedi.
Obi-Wan arrives at Mandalor to find it the center of a convocation of Separatist forces. Pretty much every known Separatist planet has representatives here; Obi-Wan even spots some aliens he had no idea were preparing to defect. Clearly, the Mandalorians are a major part of the conspiracy against the Republic. Obi-Wan sends a signal back to Coruscant, then goes to investigate further. He soon finds that he's not alone; he senses the presence of a familiar Jedi, the aged (but spry) Count...oh, does he have to be called "Dooku"? It really sounds like a Muppet of some sort. Perhaps "Doku", or "Doka." (As with "Jar Jar", we'll stick with the movie name to avoid confusion for now.) In any event, his mentor's mentor, Qui-Gon's teacher. Dooku also discovered the Mandalorians' involvement, and came to this planet to find out what the Mandalorians are providing the Separatists. He may be old, but an old Jedi is a Jedi nonetheless.
Anakin and Amidala have fled further out from Boba Fett's pursuit, out near the Outer Rim (where Anakin and Obi-Wan have just spent the last few years, learning the territory almost as well as a native.) Despite the danger, or perhaps because of it, the two are drawn together and Amidala admits that she missed him more than she's been willing to say. He suggests that maybe, when the danger is over, they could have a real relationship, as man and woman instead of Queen and Jedi...but Amidala doubts it would ever happen. She cannot stop being a queen (because they're not elected...) and his commitment to the Jedi order is not lightly broken. Anakin refuses to give up his dreams, but the conversation remains unfinished as they pick up a signal from a Republic ship, a rarity in this sector of space. The transmission was intended for Coruscant, but it has been partially blocked, its signal strength reduced to the point where it could never have reached the Republic homeworld. (Yeah, one guess as to who it's from. Look one paragraph up.)
Obi-Wan and Dooku continue searching for the Mandalorians' secret, and they find it. Oh, wow do they find it...an entire army of clones, produced on a secret clone factory elsewhere in the Outer Rim, and all equipped with Mandalorian weaponry. Turns out Boba Fett is just the most accomplished Mandalorian warrior, not the only one by far. Obi-Wan tells Dooku that they need to find the location of the Mandalorian cloneworld, or the Republic may be in dire peril. Dooku spins, placing his lightsaber against Obi-Wan's throat. "I know exactly where it is," he says.
Now a captive, Obi-Wan rails against Dooku's betrayal. Dooku explains that the Republic has grown corrupt, that sinister forces have gained play even in its very heart. He believes that Obi-Wan can help, though. If Obi-Wan agrees to become his apprentice, to learn new, secret techniques that Dooku has mastered, perhaps they can together rebuild the Republic as something worth fighting for. Obi-Wan refuses, but Dooku points out that he has nothing but time to consider the offer, now.
Things more or less follow the original movie from here. Anakin and Amidala go to rescue Obi-Wan, and get in over their heads. (No giant Roman gladiatorial arena, though. Just an increasingly desperate series of battles, as Amidala finds out that she's a target due to her symbolic value as Queen of Naboo, where the civil war first began.) Anakin reveals that he called for reinforcements before going to help Obi-Wan, and Jedi show up to save the day. Then the Jedi get in over their heads, and the entire Republic army shows up to save the day. Dooku escapes after a battle with Obi-Wan, Anakin, and Yoda (yes, I'm keeping the Yoda battle; I'm a huge Hong Kong movie fan, and the whole "old master looks frail and feeble but seriously kicks ass" trope is one of my favorites.) The Republic wins a battle, but much of the Separatist army manages to retreat, and no prisoners seem to know the location of the secret cloneworld. The Clone Wars begin.
And back on Coruscant, Dooku lands a secret craft in the heart of the Republic. He confers with Darth Sidious, who calls him "Darth Tyrannus" and compares notes with him on their plan to create a civil war in the Republic. "Soon, the Jedi will fall..." Sidious notes, taking off his hood, "and the dominion of the Sith will be complete." And Dooku smiles as he and Chancellor Palpatine part ways to plot the downfall of a Republic.