One great fanfic could be 'Pretending for Love'. In this fic, their fake dating starts as a way to solve a work - related problem but soon turns into something more complex. They start to develop real feelings in the midst of all the pretend kisses and dates. It's a really sweet read.
Another interesting plot twist could be that their fake dating is discovered by an enemy who then tries to use it against them. So they have to either come clean or double down on their fake relationship to deceive the enemy. This adds a whole new layer of drama and tension to the story.
I really like 'The Bond Between Alex and Maggie'. This fanfic delves deep into their individual backstories and how those experiences shape their relationship. It shows how their different personalities complement each other, like Alex's seriousness and Maggie's more laid - back nature coming together in a really interesting way.
Fanfiction.net is another place. It has been around for a long time and has a lot of fan - created content. There may be some great Alex and Maggie fanfics there too. However, the interface might not be as user - friendly as AO3, but it's still worth checking out.
I'd recommend 'The Danvers Sisters' Journey'. It focuses on their growth as individuals and as sisters. It has some really heartwarming moments, like when they have late - night talks and share their deepest fears. It also shows how they deal with the villains in their own unique ways, all while strengthening their relationship.
One possible fanfic could focus on a mission gone wrong that leads to both Alex and Kara experiencing PTSD. In the story, they might initially try to hide their symptoms from each other. Kara could be having nightmares about not being able to save the people she loves during the mission, while Alex might be jumpy and overly vigilant. As the story progresses, they finally open up to each other and start to heal together, perhaps through some shared training sessions that also double as therapy, where they learn to trust themselves and each other again.
A good 'Alex Danvers and Kara Danvers Fanfic' has to capture their unique relationship. Since they are sisters, it should show the love, bickering, and support that comes with that. For example, if it has a scene where Alex is training Kara and is tough on her but also encourages her, that's great.