I have three big bads.
The first and most immediately obvious big bad is Legate Ceres, the supreme ruler of the separatist movement called the League of Sovereign Planets. She leads the charge against the Republic in the Clone Wars, severing the head of the Republic in the war's very first battle (by all accounts a tactical victory). A dark side-corrupted Jedi, her interactions with Anakin Skywalker prove to be of critical importance in the tale being told in my prequels. She is the white whale to Skywalker's Moby Dick. But even in death, she attains a spiritual victory. Though her League armies ultimately lose the Clone Wars, she wins in a way only the dark side of the Force can claim a victory: through corruption of the opponent's character...in this case of the Jedi Knight Anakin Skywalker. Ceres appears in Episode I: In the Age of the Jedi and Episode II: The Dark Times Begin.
The second big bad is Admiral Palpatine, founder of the Galactic Empire. A charisma afforded to him by the dark side of the Force allows him to unite large swaths of a scarred galaxy under his dark ideology: the right of the strong (Human) species to rule over the rest. In pre-Clone War times he was the Vice Chief Officer of the Republic Navy, constantly using his dark side powers to scheme and plot as the "power behind the throne", never seeking to be put "on the spot" politically. But his delusions of grandeur after Ceres' brazen attack on Coruscant and the subsequent collapse of the Republic allow him to take control of his homeworld of Anaxes and use it as a base of operations to forge an empire of dominance and strength, but at the cost of any and all humanity. It is he who convinces Anakin Skywalker that the dark side could provide order to a galaxy in turmoil. Palpatine only appears in Episode II.
The final big bad is Anakin Skywalker, and indeed the big bad that the entire series has been building up to. It is not until the final act of Episode II, that Anakin finally becomes convinced that the dark side of the Force is the only way to bring order to the galaxy. But near the end Episode III, the full extent of Anakin's madness is revealed. He kidnaps the mother of his children, Jeni, and locks her down on the fortress world of Had Abaddon so that she can carry her twins to term, thus providing Anakin with the genetic crop to start a new dark Jedi order with which to overthrow Palpatine and rule the galaxy as a new dynasty of darkness. The final mission of our heroes is to break into the Had Abaddon Imperial fortress and rescue Jeni from the clutches of the traitorous Anakin Skywalker. While Anakin himself appears in all three prequels, his "big bad" role is only fulfilled at the end of Episode II and all throughout Episode III: War of the Skywalkers.
We never see the famous black armor suit, nor is the name "Darth Vader" ever uttered in the trilogy, but I do my best to imply that this Anakin Skywalker is in fact the same man as the one who strikes down Ben Kenobi in cold blood on the first Death Star.
Likewise, we do *not* see Palpatine use Force Lightning at any point in his screen-time during Episode II. He is shown to be gifted in use of the Force in other ways.