Perhaps in the fanfic world, there are some magical or supernatural elements at play. Maybe there is a spell or a charm that is making Magnus act strangely, but Alec doesn't know about it. Alec could be misinterpreting Magnus' actions because of this. Also, if there are new characters in the story that seem to have a special connection with Magnus, Alec might jump to the conclusion that Magnus is cheating.
Maybe Alec noticed Magnus being secretive about his phone or meetings. If Magnus is suddenly cancelling their plans often without proper explanation, it could make Alec suspicious. Also, if Magnus is overly friendly with someone else in a way that seems inappropriate, like getting too close or sharing personal things that he usually only shares with Alec.
One possible reason could be that Magnus has been spending a lot of time away from Alec. Maybe he has been staying out late at night without a proper explanation. Another reason might be that Magnus has been secretive about his phone or messages. Alec could have seen Magnus being a bit too friendly with someone else, which made him start to suspect cheating.
They need to have an open and honest conversation. Magnus should explain his actions clearly to Alec. If there are any misunderstandings, they can be cleared up right away.
In the context of a fanfic, Magnus might use his magic in a positive way. He could create a magical bond or a truth - revealing spell between him and Alec (with Alec's consent, of course). This would allow Alec to see into Magnus' thoughts and feelings, and he would know for sure that Magnus is not cheating. Magnus could also start spending more time with Alec and less time on his own or with other people, at least until Alec's suspicions are completely gone.
One reason could be miscommunication. Maybe they didn't fully understand each other's needs and wants. For example, Alec might be too focused on his shadowhunter duties and not give enough time to Magnus, who would then feel neglected.
One common way could be through using his magic in a subtle way. For example, he might use magic to create situations where Alec has no choice but to follow his lead. Maybe he makes it seem like the only option for Alec to protect his friends or family is to do what Magnus wants.
One characteristic is the focus on the relationship between Alec and Magnus. It could be their romantic relationship, like in many fanfics where their love story is explored in great detail. Another is the exploration of their individual personalities. For instance, Alec's loyalty and Magnus's magic are often highlighted.
Perhaps there have been some rumors or whispers in their fictional world that have reached Alexis' ears. Even if they are baseless, they can plant the seed of doubt in Alexis' mind, making her think that Kate is cheating.
Maybe he saw Beckett spending a lot of time with another man without knowing it was for a case. Castle is a bit of a jealous type, and he might overreact to normal interactions.
He may also try to reason with Magnus or the kidnappers. Alec is a smart guy, so he might try to find a way to get out of the situation through dialogue. He could point out the negative impacts of their actions on everyone involved.
Love is a very common theme. Their relationship, which is between a Shadowhunter and a warlock, is full of challenges and the fanfics often explore how they overcome these through love. Another theme is acceptance. Alec has to accept Magnus's different lifestyle as a warlock, and Magnus has to accept Alec's duties as a Shadowhunter.