Perhaps an ancient evil spirit that was sealed away long ago. The hatching of the legendary starter's egg is a sign that the spirit can break free. It wants to possess the starter to regain its full power and take over the Pokemon world. This would make for a very dark and menacing antagonist, and Ash would have to use all his skills and the power of his friendship to defeat it.
Obviously, Ash is one of the main characters. He is the trainer who gets the legendary starter. And of course, the legendary starter itself is also a main character. It has its own personality and abilities that play a big role in the story.
It could be Team Rocket. They are always after rare and powerful pokemon. In this fanfiction, they might have a new and devious plan to steal the legendary pokemon that Ash is trying to catch. Their comical yet persistent attempts to thwart Ash would add an interesting dynamic to the story.
Team Rocket could still be the main antagonists. Even though they usually have comical failures, in this fanfiction, they could discover Ash's connection to the legendary Pokemon and try to use it for their own evil plans. Maybe they want to capture the legendary Pokemon through Ash or steal the power that Ash has because of his chosen - one status.
Perhaps a dark - themed Pokémon organization that is researching the unique powers of Mudkip. They see Ash's Mudkip as a key to their experiments. So they send out their agents to capture it. These agents are skilled trainers with powerful Pokémon at their disposal, and they constantly pose a threat to Ash and his Mudkip throughout the fanfiction.
In a fanfiction like this, the plot could revolve around the fact that the egg is the key to restoring balance in the Pokemon world. The legendary starter that hatches from it is initially weak but grows rapidly under Ash's care. However, there are forces at work that want to use the starter for their own evil gains. Ash has to team up with his friends and other Pokemon to fend off these threats. The story could also explore the relationship between Ash and the legendary starter as it grows, how they learn from each other, and how their bond becomes unbreakable.
Team Rocket would be the most obvious ones. They're always after rare and powerful Pokémon or Pokémon - related items, so the legendary egg would be a huge target for them.
Another possibility is that an old rival of Ash's, who has always been jealous of his success, becomes the main antagonist in this fanfiction. When Ash chooses a different starter, this rival sees it as an opportunity to finally defeat him, thinking that Ash's new and untested starter will be his downfall.
It could be a trainer who has a starter that has a type advantage over Ash's new starter. For example, if Ash has a Squirtle and the antagonist has an electric - type starter like Pikachu, they would constantly be in conflict. The antagonist might be jealous of Ash's skills or the potential of his Squirtle and try to undermine him at every turn.
Team Rocket could be the main antagonists. They might hear about Ash's encounter with Mew and try to capture Mew for their own evil plans. They could set up all sorts of traps and schemes to try and separate Ash from Mew and steal Mew away.
Well, in this kind of fanfiction, Ash might take really good care of the egg. He could keep it warm and protected all the time. Maybe he'd build a special nest for it. And when it hatches, it could be a super powerful legendary Pokémon that immediately bonds with Ash and helps him in his Pokémon journey.