Every story has a primary antagonist. There may be a few lesser bad guys, either under their command or unrelated to them entirely, but there's always one final big bad at the end that needs to be dealt with. Many stories set these antagonists up fairly early on, sometimes for the sake of quick character motivations, other times for another purpose.
Sometimes, the character that seemed like the biggest bad of the bunch ends up being an unwitting second fiddle to an even greater evil. These reveals can happen at any time in the story, be it near the beginning, in the middle, or even at the very last minute.
8 Maleficent And Ansem - Kingdom Hearts
Early on in Kingdom Hearts' story, Maleficent, alongside her council of Disney Villains, is set up as the instigator of the Heartless invasion and the ultimate threat to the worlds' safety. However, a much more complicated plan was running behind the scenes, and its architect was none other than Ansem, Seeker of Darkness. Maleficent did let the Heartless loose, as well as conditioned Riku into allowing darkness into his heart. Still, she had no idea that Ansem would use that opportunity to secure a vessel for himself.
It's not entirely clear to what extent Maleficent was aware of Ansem's meddling. Knowing her, she probably just assumed that Riku had bought what she was selling and given himself over fully to the darkness. That gap in her judgment allowed Ansem to unleash the darkness in her own heart and ultimately supersede her as the master of the Heartless.
7 The Syndicate And STAG - Saints Row The Third
For the majority of Saints Row The Third, the Saints' primary enemies are the various subdivisions of the Syndicate. As the Saints tear through the Morningstar, Deckers, and Luchadores, they inadvertently make a case for launching the Special Tactical Anti-Gang unit, also known as STAG. When the Luchadores blow up a bridge to pick a fight with the Saints, that's the last straw.
While the Saints still tangle with the Syndicate, particularly Luchadores leader Killbane, STAG begins taking greater precedence, locking down Steelport with their flying aircraft carrier. This ultimately culminates in their second-in-command, Kia, kidnapping Shaundi and the Mayor. It's up to the Boss whether they rescue them or pursue Killbane, but it's worth noting that the former option is the canon choice.
6 Eggman And Gerald Robotnik - Sonic Adventure 2
When Eggman first frees Shadow from confinement at the beginning of Sonic Adventure 2, Shadow offers him control of the Eclipse Cannon aboard the Space Colony ARK. With the cannon's power, Eggman would have the ultimate bargaining chip to control the world. However, when all the Chaos Emeralds were placed in the cannon's core, rather than activating it, it triggered a special program.
Shadow's deal with Eggman was orchestrated decades in advance by Eggman's own grandfather, Dr. Gerald Robotnik. Mad with grief at the death of his granddaughter Maria at the hands of GUN, Gerald programmed the ARK to enter a crash course with the Earth once the Emeralds were gathered. The plan was so elaborate that Gerald managed to arrange the entire thing posthumously.
5 Shinra And Sephiroth - Final Fantasy 7
For the first chunk of Final Fantasy 7's story, particularly the part set in Midgar, the Shinra Electric Power Company is the first and foremost threat. Avalanche organizes various bombings and attacks to destroy their reactors and infrastructure and stop their Mako-draining efforts from damaging the planet. The situation becomes much more serious when Aerith is kidnapped by President Shinra, prompting Cloud and company to storm Shinra HQ.
When they arrive at the top, however, they find President Shinra dead at the hands of legendary SOLDIER, Sephiroth. At this point, Sephiroth is revealed as the true main antagonist of the story, as he seeks to obtain Black Materia to summon a Meteor to the Earth. When the Meteor damages the planet, he enters the resulting Lifestream leak and becomes a godlike being.
4 Zant And Ganondorf - The Legend Of Zelda: Twilight Princess
Not long after the veil of Twilight began to blanket Hyrule in The Legend of Zelda: Twilight Princess, the supposed King of Twilight, Zant, reveals himself. Zant has a longstanding grudge against the denizens of the realm of light for imprisoning the Twili people in the Twilight Realm and seeks to conquer Hyrule in the Twili's name. In actuality, that entire set-up is more of a loose justification that Zant himself came up with.
Zant was one of the candidates for the ruler of the Twilight Realm, but he was passed over in favor of Midna due to his scheming ways. In the midst of a wild tantrum, Zant was touched by the wayward spirit of Ganondorf, gaining the power necessary to stage a coup. Ganondorf didn't really care that much about Zant or the Twilight Realm, which is why the "king" was ultimately disposable. All Ganondorf wanted was a way back to Hyrule so he could take his revenge.
3 Richter And Shaft - Castlevania: Symphony Of The Night
When Castlevania reappears from the shadows, Dracula's half-human son, Alucard, storms the castle to halt any potential wrongdoings his father may have planned. Imagine his surprise, then, when the lord of the castle turns out to be none other than Richter Belmont, who had gone missing in the time since Castlevania's last appearance. Richter boasts that he plans to revive Dracula so they can battle one another for all eternity.
Of course, this isn't something Richter would do if he were in his right mind. After knocking Richter out, Alucard uncovers the true architect of the plan: the Dark Priest, Shaft. Using his magic, he manipulated Richter into assuming control of Castlevania, hoping that he and the rest of the Belmont clan would destroy each other. With the Belmonts gone, Shaft could resurrect Dracula and plunge the world into chaos unopposed.
2 Shido And Yaldabaoth - Persona 5
The first few Palaces raided by the Phantom Thieves in Persona 5 didn't have any particular overseer to them. They were merely a handful of instances of particularly warped cognition in need of a change of heart. Soon enough, though, it became clear that many of these individuals were under the direct command of politician Masayoshi Shido, who used the Metaverse to conquer Japan in secret.
Shido's goals, however, were relatively small in the grand scheme of things. His plan, along with Akechi and Joker being granted access to the Metaverse, was part of a grand design by Yaldabaoth, a cognitive entity formed from humanity's longing to be controlled and commanded. In Yaldabaoth's eyes, Shido's plan and defeat at the hands of the Phantom Thieves were proof positive that humanity needed a governing entity, and he used the Metaverse to exert his control over the collective cognition directly.
1 Mister Negative And Doctor Octopus - Marvel's Spider-Man
For the first major arc of the story of Marvel's Spider-Man, the primary villain is Martin Li, AKA Mister Negative. Li assembled the Demons gang and committed various terrorist attacks around New York City with the intent of discrediting and, ultimately, killing Mayor Norman Osborn. Spider-Man stopped his plan, but Web-Head's focus on Li meant he missed a greater threat right next to him.
Following Li's arrest, he and four other villains were broken out of Ryker's Island by Peter's friend and coworker, Doctor Otto Octavius, AKA Doctor Octopus. The neural interface used to control Ock's tentacles exasperated an existing grudge he had against Osborn himself. When the opportunity to get back at Osborn presented itself, he wasted no time assuming the reins.