Maybe there's an ancient evil that has been dormant for a long time. The prophecy of Hiccup and Elsa's child awakens this evil. It sees the unborn child as a threat to its plans of world domination. So it sends its minions to attack Elsa and Hiccup. These minions constantly harass them during Elsa's pregnancy, making it difficult for them to find a safe place and prepare for the arrival of the baby.
One possible antagonist could be a jealous sorcerer. He might be envious of Hiccup and Elsa's relationship and the power that their unborn child is said to possess. So he tries to harm Elsa during her pregnancy to stop the child from being born. Another could be some of the traditionalists from their respective kingdoms. They don't approve of their relationship and see the pregnancy as a threat to their old ways. They might try to separate Hiccup and Elsa, which would put Elsa's pregnancy at risk.
A group of dark magic users could be antagonists. They believe that the child of Hiccup and Elsa will disrupt the balance of magic in the world, but in a negative way according to their twisted view. They plot to kidnap Elsa and perform dark spells on her to end the pregnancy. Also, an old enemy of Hiccup's family might see this as an opportunity to get revenge on Hiccup by targeting Elsa and the baby.
Well, perhaps a power - hungry wizard from a neighboring magical realm. He hears about the baby's unique powers that combine Jack Frost's and Elsa's abilities and wants to harness that power for his own evil plans. Or it could be a group of dark fairies who are envious of the baby's special connection to both the winter world and Arendelle. They might try to kidnap the baby and raise it to be on their side, away from Jack and Elsa.
There could be an old dragon that has been in exile for a long time. This dragon might see Hiccup as a threat to its plan of taking over the dragon kingdom. So it tries to stop Hiccup from fully becoming a dragon or tries to use his new form for its own evil purposes.
A group of dragon hunters who don't believe in Hiccup's divinity could be antagonists. They think that dragons should be under their control, not Hiccup's. So they set out to capture all the dragons and overthrow Hiccup. They might use new and dangerous weapons to achieve their goals.
Perhaps it could be Kristoff. Although he was more interested in Anna in the original story, in fanfiction, the relationships can be reimagined. They could have developed a closer bond over time and he could be the father.
One possible plot could be that Hiccup, while on a journey with Toothless, somehow gets transported to Elsa's world. He stumbles upon Elsa as she is trying to control her powers in a difficult situation. Hiccup, with his experience dealing with dragons, offers her a different perspective on handling her powers. They gradually grow closer as they share their stories and in a moment of deep connection, they share a kiss.
The Brotherhood of Mutants could also be antagonists. They might view the pregnancy as a sign of the X - Men becoming too domesticated and vulnerable. They could launch attacks on the X - Mansion in an attempt to disrupt Rogue and Logan's new - found family situation.
Maybe there are some traditionalists in their world who don't approve of their relationship or the pregnancy. These people could be the antagonists, constantly trying to break them apart or cause problems for them.
One potential antagonist could be a group of rogue ninjas who see Sarada's pregnancy as a sign of weakness in the village. They might try to target her to cause chaos. Another could be a jealous rival who doesn't like the attention Sarada is getting due to her pregnancy and her connection to Naruto.
Frieza or his remnants could be antagonists. They might see the unborn child as a potential threat in the future, especially if it has strong Saiyan powers. So they could plan to attack Bulma to prevent the birth.
The Vicious 6 could be the antagonists. They might see Gru's preoccupation with Lucy's pregnancy as a weakness and try to take advantage of it. They could plan to kidnap Lucy to get to Gru and force him to give up his new - found family life and return to his old villainous ways.