A mad scientist could be the main antagonist. He wants to capture the wolf for further experiments. He sees the wolf as a perfect specimen for his inhumane research. Alex Rider has to stop him from getting his hands on the wolf and also expose his evil plans to the world.
Perhaps a shadowy organization that wants to use the wolf as a weapon. They believe that by controlling the wolf, they can gain an edge in their global domination plans. Alex Rider discovers their plot and teams up with the wolf to take on this powerful and dangerous organization.
It could be a poacher who is after the wolf for its unique fur or some body part that he believes has special powers. He would be constantly trying to hunt the wolf down, which would put him in direct conflict with Alex Rider who is protecting the wolf.
It could be a powerful and shadowy figure from Wolf's past, like an old military commander who has gone rogue. This person might have a vendetta against Wolf for some past betrayal and sees Alex as a way to get to Wolf, using Alex's importance in the spy world as leverage.
One possible plot could be that Alex Rider is on a mission in a forested area and he stumbles upon a wolf. Instead of the wolf being hostile, it seems to have an unusual intelligence. Alex discovers that the wolf is actually a genetically modified creature, part of a secret experiment. They form an unlikely alliance to take down the organization behind the unethical experiments.
A good antagonist could be a character from the 'Resident Evil' universe, like Albert Wesker. His superhuman abilities and evil plans for global domination would pose a huge threat to Alex Rider. Alex would have to use his wits and skills to stop Wesker's bio - terrorist plans.
Perhaps Mister Sinister. He has always been interested in mutants like Wolverine and could see Deadpool as a useful pawn or a nuisance in his grand schemes. He might try to manipulate the situation to his advantage, causing Deadpool and Wolverine to join forces against him.
It could be a powerful, corrupted Pokemon trainer who wants to capture Cosmog and use its unique powers for his own evil purposes. He might see Cosmog as a key to unlocking ultimate power and doesn't care about the harm it could cause to Cosmog or the Pokemon world. He could also be in league with some dark - type Pokemon that can create obstacles for Marshadow and Cosmog.
Mr. Burns could potentially be the antagonist. He might see the combination of Spongebob and Homer as a threat to his power in Springfield. He could try to separate them and cause trouble for them. Maybe he wants to take over Bikini Bottom as well, seeing it as a new source of resources or power. He starts by spreading rumors about Spongebob and Homer in both their hometowns to turn the locals against them.
It could be Darth Sidious. Since he is always looking for power and control in the Star Wars universe, he might see Naruto as a threat to his plans when Naruto arrives in Padme's world. He would try to eliminate Naruto and use Padme as a pawn in his political games.
It could be Ra's al Ghul. He's always interested in things that can give him an edge in his quest for immortality. If he discovers the power of chakra in the Naruto world, he might try to take over both worlds. His skills as a master assassin and his vast resources would pose a huge threat to Naruto and Batman, who would have to put aside their differences to defeat him.
It could be a power - hungry ninja from within the Hidden Cloud Village who sees Raikage's relationship with Hinata as a threat to his own plans for taking over the village. He might try to spread false rumors about Hinata being a spy to turn the villagers against her and the Raikage.
A powerful dark ninja who has made a pact with some dark force from another dimension. He sees Gabriel as an intruder and Naruto as a threat to his plans of taking over the ninja world. He would use his dark jutsu and the power from the other dimension to oppose Naruto and Gabriel, and would stop at nothing to achieve his goals.