Chancellor Palpatine played the long game in the Star Wars prequel trilogy, using both the Republic and the Separatists to orchestrate the downfall of the Jedi Order. The Sith Lord's endgame finally came to fruition in Revenge of the Sith, wherein he corrupted Anakin Skywalker, used the clone troopers to kill all the Jedi, and consolidated the Republic into a new Galactic Empire.
As masterful as Palpatine's plan ultimately was, it wasn't completely infallible. If the wrong person discovered his true motives, everything that Palpatine had built would have crumbled before his eyes. Yet, several characters nearly foiled his plot prior to the events of Revenge of the Sith, only to be quickly swept under the rug by the scheming Sith Lord.
10 Yaddle
Yaddle was a Jedi Master serving on the High Council in 32 BBY, during the events of The Phantom Menace. However, she disappears prior to the events of Attack of the Clones ten years later. While Star Wars came up with many explanations for the Jedi's disappearance over the years, Tales of the Jedi finally revealed that she had been killed after discovering part of Darth Sidious's plan.
Shortly after Qui-Gon Jinn's death, Yaddle became suspicious of his master, Dooku, who had secretly begun training as a Sith Lord. She followed Dooku to a secret meeting with Sidious, overhearing their plan to overthrow the Jedi. Had she been able to escape, Yaddle might have prevented the eventual downfall of the Jedi, but was killed by Dooku instead.
9 Darth Maul
Darth Maul, the former Sith Apprentice of Darth Sidious, became disillusioned by his master's plotting after his return from the dead. In the final episodes of The Clone Wars, Maul is revealed to have had a vision about Anakin Skywalker turning to the dark side and bringing about the fall of the Jedi.
Maul invades Mandalore as a way of drawing out Obi-Wan Kenobi to tell him of his vision but instead attracts Ahsoka Tano. He tries to form an alliance with Ahsoka against Palpatine, but she refuses. Only a few hours later, Order 66 goes into effect and Anakin is turned, proving Maul's vision correct.
8 Count Dooku
Count Dooku was one of the few people in the galaxy who knew the truth about Chancellor Palpatine--that he was secretly the Sith Lord Darth Sidious. Although Dooku worked for Sidious, he, like many other Siths throughout the years, secretly plotted against his master.
Beginning with their first meeting in Attack of the Clones, Dooku repeatedly reached out to Obi-Wan Kenobi in an attempt to form an alliance with him against Sidious. Dooku's plan was to overthrow Sidious and the Republic in order to create a better galaxy. Unfortunately for him, Dooku himself was a pawn who was easy for Sidious to replace.
7 Mon Mothma
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Mon Mothma barely has any presence in the prequel trilogy, but does appear in several deleted scenes from Revenge of the Sith. In these cut scenes, the Chandrillan Senator is part of a leading group of politicians who take issue with Chancellor Palpatine's actions. Prior to the Empire's formation, these senators attempted to remove Palpatine from office.
Among this secret group were Mothma, Bail Organa, and Padme Amidala. Although they were unable to act in time to prevent Palpatine's siege of power, their efforts did lay the groundwork for the future Rebellion against the Empire.
6 Padme Amidala
Although Palpatine may have wanted Senator Padme Amidala dead during the events of Attack of the Clones, he eventually came to see her as a key tool in his plan. After Anakin Skywalker fell in love with the senator, he would do anything to protect her--including turning to the Dark Side.
Unfortunately for Palpatine, Padme was also the only person who stood a chance of talking Anakin out of his descent. She reached out to her husband on Mustafar in an attempt to make him see reason after his turn. While she may have been able to change his mind, Anakin was distracted by the appearance of Obi-Wan Kenobi, cementing his downfall.
5 Tup
CT-5385, also known as "Tup," was a member of the 501st Legion during the Clone Wars. Shortly before Order 66, Tup went into a strange episode wherein he suddenly killed Jedi General Tiplar in the middle of a battle. Worried about a defect in their programming, the Kaminoans put Tup under observation immediately.
Tup's episode was eventually revealed to be the result of his malfunctioning inhibitor chip--something that no one was aware the clones had. This inhibitor chip had been secretly commissioned by Palpatine to key Kaminoans to ensure the clones would obey Order 66 and kill the Jedi when the time came. Tup's malfunctioning chip nearly alerted the Republic to the truth about the clones early, which could have potentially averted the Great Jedi Purge.
4 Yoda
Master Yoda becomes Palpatine's fiercest opponent after the Great Jedi Purge. Having survived Order 66 on Kashyyyk, Yoda travels to Coruscant with Obi-Wan Kenobi to defeat the Sith once and for all. Yoda and Palpatine duel in the Senatorial chamber, each showing off his immense strength.
Palpatine eventually defeated Yoda during their battle, but his victory was hard-won. Yoda clearly had the power to overthrow the villainous Sith Lord, but was unfortunately outmaneuvered in the end. Had the battle gone differently, however, Palpatine's reign may have been cut mercifully short.
3 Fives
CT-5555, also known as "Fives," was an Arc Trooper in the 501st Legion during the Clone Wars. After his companion, Tup, shockingly murdered a Jedi, Fives begins to investigate what could have made a good clone snap. He eventually uncovers the truth about the clones' inhibitor chips--which make them incapable of resisting the order to murder their Jedi Generals.
Fives is the one person to discover the truth about Order 66 and desperately tries to alert his fellow clones and the Jedi. No one believes him, driving him to other allies. Unfortunately for Fives, he brings this information to Chancellor Palpatine, unaware that he is the very person behind the inhibitor chips. Palpatine ensures that Fives is dealt with swiftly, preserving his plan.
2 The Jedi Council
Although the Jedi Council remained unaware that Chancellor Palpatine was actually a Sith Lord for the duration of the Clone Wars, the Jedi Masters never truly trusted him. In the opening act of Revenge of the Sith, Obi-Wan reveals to Anakin that the Council wants to spy on the Chancellor to discover what his true motivations are.
Had Anakin agreed to spy on Palpatine for the Jedi, they might have discovered the truth about his allegiances and stopped him before he did any more damage. Upon finally learning that he was a Sith Lord, the Jedi Council resolved to arrest Palpatine, but it was already too late and they were swiftly executed.
1 Anakin Skywalker
Anakin Skywalker was the linchpin of Palpatine's plan to overthrow the Jedi. Using his own emotions against him, Palpatine slowly turned Anakin to the Dark Side, renaming him Darth Vader. However, Anakin very nearly refused to join Palpatine in Revenge of the Sith.
Upon first discovering the truth, Anakin is inclined to kill Palpatine where he stands and even turns him over to the Jedi Council. Had he remained content with his decision, Anakin would have brought Palpatine's plot to an early end. However, his own love for Padme betrayed him, leading him to align himself with Palpatine in order to save her life--thereby dooming the Jedi and giving the Sith Lord precisely what he had wanted all along.