Maybe it's a new character created specifically for this fanfiction. A powerful alien scientist who sees Morty and young Rick as a threat to his plans for universal domination. He would constantly be trying to stop their adventures and capture them.
There's a possibility that an older Morty from a different timeline becomes the antagonist. He's bitter about his own life and doesn't want this Morty to have a good time with young Rick, so he tries to disrupt their relationship and the positive experiences they're having.
In this fanfiction, Morty might be really shocked at first to meet a young Rick. He could be confused about how this young version of Rick behaves compared to the Rick he knows. Maybe they'll go on some wacky adventures together that are different from the ones Morty has with the regular Rick.
The League of Shadows could be a great antagonist. They might see Young Justice as a threat to their plans in the world and Batgirl as an obstacle in Gotham. They could try to manipulate situations to make Young Justice and Batgirl turn against each other while they carry out their own devious plans, like releasing a dangerous virus in a major city.
It could be a new group of survivors who are extremely territorial. They see Rick's group and Clementine as threats to their resources. This group might be led by a power - hungry man who is willing to do anything to protect what he thinks is his, including attacking Rick's group and trying to capture Clementine.
Well, in the world of fanfiction, people can take characters in all sorts of directions. But in the context of 'Rick and Morty', the idea of Rick abusing Morty in the fanfiction is a deviation from the show. The show focuses on their interdependent relationship, with Rick being the brilliant but flawed mentor and Morty being the somewhat naive sidekick. Fanfiction writers might create such scenarios to explore the darker side of their relationship, but it's not a part of the main narrative.
It could be some alien she met during one of Rick's adventures. Maybe she got involved with a being from a different dimension who had a human - like form and they had a brief encounter that led to the pregnancy.
Some writers might create this type of fanfiction for shock value. They know that the original relationship between Rick and Morty has a certain dynamic, and by making it into an abusive one, they can get a strong reaction from readers. Also, it could be a form of expressing their own dark interpretations of power dynamics within the show.
There could be an ancient force that is awakened by the meeting of Harry and Hela. This force wants to destroy both of them because their combined powers could potentially stop it from achieving its goal of spreading chaos and destruction throughout all the realms. It would use all kinds of devious means to try and separate them and defeat them one by one.
Maybe a powerful warlord from Negan's world who somehow follows him into Artemis' realm. This warlord, with his own thirst for power and destruction, would oppose both Negan (if he starts to side with Artemis) and Artemis herself, wanting to take over the new world he has found.
It could be another god who is jealous of Zeus' interest in Atreus. Maybe a god who feels that Atreus is an outsider and doesn't belong in their divine affairs.
Another possibility is that Death is being controlled or influenced by a greater cosmic entity. In this case, that entity could be the main antagonist. It uses Death as a tool to test or destroy the Avengers. The Avengers would then have to not only deal with Death but also find a way to face this more powerful and mysterious entity behind Death's actions.