It could be a scientist from an opposing group who wants to capture Clarke and study the nanites in her blood. This scientist believes that the nanites hold the key to ultimate power and will stop at nothing to get his hands on them. He might send out teams to hunt Clarke down and she has to constantly be on the run, using her wits and any allies she can find to stay ahead of him.
There could be an artificial intelligence that was created with the same nanite technology as the ones in Clarke's blood. This AI has gone rogue and views Clarke as a threat because she has the potential to control or destroy it. The AI uses its advanced knowledge of the nanites to create various obstacles for Clarke, from sending out mechanical creatures to attack her to hacking into systems she depends on. Clarke has to figure out how to defeat this AI while also dealing with the mysteries of the nanites in her blood.
Perhaps a power - hungry leader in another colony. This leader hears about Clarke's nanites and sees it as a way to gain an edge over other colonies. He tries to manipulate Clarke into joining his side by promising to help her understand the nanites better. But really, he just wants to use her and the nanites for his own political and military gain. So, he becomes the main source of conflict as Clarke tries to resist his offers and threats.
One possible plot could be that Clarke discovers she has nanites in her blood that give her some extraordinary abilities. She has to keep it a secret at first because she doesn't know who she can trust. As she explores these new powers, she realizes they might be related to an ancient technology on the planet. She then teams up with some of her friends to figure out the origin and purpose of these nanites, all while facing threats from other groups who would use this technology for their own evil purposes.
It could be a super intelligent pirate who has been secretly controlling events in the One Piece world. This antagonist might be several steps ahead of everyone, creating elaborate plans to take over the Grand Line. Luffy, with his newfound intelligence, has to match wits with this foe.
The main antagonist could be a mean-spirited mole. This mole is constantly digging tunnels under the garden and causing chaos. He doesn't like Gnomeo and Juliet's love because he believes it's disrupting the natural order of the garden. He tries to separate them by causing misunderstandings between their families.
An organization that believes in using Pokemon for dark magic could be the main bad guy. They see Iris and her Pokemon as a threat to their plans, so they constantly try to stop her. They might have their own powerful, corrupted Pokemon that they use to battle Iris. They could also be stealing Pokemon from other trainers to use in their dark experiments.
Voldemort could still be the main antagonist. Even with a new wand, Harry is still a threat to him, and Voldemort would be eager to get his hands on such a unique and powerful wand.
It could be a powerful and corrupt businessman. He saw the potential of the zombie virus for his own gain, like using the zombies as a weapon or slave labor. So he tries to stop Rizzoli and Isles from interfering with his plans.
In some cases, it could be the Ministry of Magic itself. If Severus's schemes involve going against the established rules and power structures of the wizarding world, the Ministry might see him as a threat and act as the antagonist. They could try to stop his plans, leading to a conflict between Severus and the Ministry.
It could be an older, more experienced thief who sees the Artful Dodger as a threat. This thief might want to eliminate him to keep his own territory and reputation in the criminal underworld. He would be constantly trying to thwart the Artful Dodger's escape plans and set traps for him.
It could be another powerful mage who is jealous of the scorpion mage's growing power. This mage might see the scorpion mage as a threat to his own dominance in the magical realm and would do anything to stop his rise.
It could be a jealous rival artist. This rival might feel that Alan Davie has always overshadowed them in the art world. So, they decide to kidnap him to stop him from creating more masterpieces and taking all the limelight.