Well, it might cause a rift in their relationship. Magnus could feel hurt and betrayed, and Alec might have to go on a quest to regain his memory and repair things.
It can lead to all sorts of interesting plot developments. Maybe it causes confusion or brings them closer together.
Another theme is the struggle against prejudice. Since they are from different 'worlds' in the story, they face a lot of judgment from others, and fanfictions often deal with how they overcome this. Also, the theme of self - discovery is quite common. Both characters grow and learn more about themselves through their relationship with each other.
Love is a very common theme. Their love story, how they overcame differences to be together. Another is the theme of acceptance, like Alec accepting Magnus' warlock nature and Magnus accepting Alec's Shadowhunter duties. And also the theme of family, as they both have different family backgrounds and how they merge their families in a way.
A frequent theme is also the power dynamics. Magnus has his powerful magic, and Alec has his position in the shadowhunter world. How they balance this in their relationship is often explored. Also, the theme of family acceptance is common. Alec's family and their reactions to his relationship with Magnus are often part of the stories.
They could also have a moment of friendship while exploring new places. For instance, they visit a hidden magical realm that neither of them has been to before. They share their excitement and fears during this adventure, relying on each other for support and protection, which deepens their friendship.
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 common theme is the exploration of new relationships. The addition of an OC often creates a new dynamic between Alec and Magnus. For example, the OC could be a mediator in their relationship, helping them understand each other better.
Another theme is self - discovery. In human fanfictions, they might be on a path to find out who they are without the trappings of their original magical or shadowhunter identities. They learn about their strengths and weaknesses as normal humans.
A major theme in magnus x alec fanfiction is the exploration of power dynamics. Magnus is a powerful warlock and Alec is a shadowhunter. How they balance their different levels of power and influence in their relationship is often explored. Also, the theme of acceptance is quite prevalent. They come from different worlds, and their journey towards accepting each other's differences is a key part of many stories. For example, in some fanfictions, Alec has to come to terms with Magnus's long life and his different magical practices.
The passion is a great element. When Alec and Magnus kiss in fanfiction, it's often described with a lot of heat and intensity. It shows the strong physical attraction between them.