The main antagonists could be the same organizations they have always fought against. For example, Umbrella Corporation or any other bio - terrorist groups. These groups might see Ada's pregnancy as a weakness and try to use it against them. They could target Ada to get to Leon or try to harm the unborn child to stop Leon from interfering with their evil plans.
In a fanfiction like this, the plot could involve Ada being pregnant with a child that has some special abilities due to their unique genetic make - up. Leon and Ada then have to figure out how to keep the child safe from those who would want to use the baby for their own purposes. It could also explore their relationship growing deeper as they face this new challenge together.
One possible storyline could be that Leon and Ada find out about the pregnancy unexpectedly. They then have to deal with the challenges of their dangerous line of work while also preparing for a new life. For example, Leon might be extra protective of Ada during their missions.
Hunnigan could be a great addition. She could provide Leon with information and support from the outside, and her presence could add some tension as she might be suspicious of Ada's motives. Another good character is Wesker. His past connection to Ada could create more drama and conflict in the story. He could be a shadowy figure trying to manipulate the situation between Leon and Ada.
Elena could be an antagonist. Since she has a history with Christian, she might try to interfere with Anastasia's pregnancy, perhaps out of jealousy or a desire to maintain some control over Christian.
Another possible antagonist could be Zelena. Jealous of Belle's happiness and the new life she's bringing into the world, Zelena could try to cause trouble. She might use her magic to create false scares or difficulties during the pregnancy, like making Belle believe there are problems with the baby when there really aren't.
It could be Gabriella's over - protective father. He might think that Troy isn't ready to be a father and tries to convince Gabriella to break up with him. He believes that their pregnancy will ruin Gabriella's future and he's very strict about it, causing a lot of tension between the couple and him.
It could be some rogue ninjas who see Temari's pregnancy as a vulnerability and try to target her or Shikamaru. They might think that a pregnant Temari would be an easy target and that Shikamaru would be distracted, so they could try to carry out some evil plan against them.
One possible antagonist could be Blair. If she still has feelings for Nate, she might see Serena's pregnancy as a threat to her relationship with Nate, whether it's a real relationship or just her own feelings. So she could try to create problems between Nate and Serena during the pregnancy.
One common theme is the struggle between love and duty. Leon and Ada are often on different sides in the official stories, so fanfics explore how their feelings for each other play out against their respective missions. For example, in many fanfics, Ada has to make a choice between helping Leon and fulfilling her own tasks.
The Capitol would definitely be a main antagonist. They are always trying to control the tributes and the Hunger Games. With Katniss pregnant, they might see it as an opportunity to manipulate the situation for their own entertainment or to quell any potential uprisings. President Snow could be especially cruel in this scenario, using Katniss's pregnancy to threaten her and those she loves.