One possible plotline could be that Skye and May have a misunderstanding during a mission. Maybe Skye misinterprets May's actions as being too harsh on a civilian, and this causes a rift between them. They could start arguing and their relationship within the team becomes strained. This would lead to a lot of emotional turmoil for both characters and also affect the dynamics of the whole Agents of Shield team.
In fanfiction, their relationship could be repaired through communication. They could sit down and have an honest conversation about what went wrong. Skye could explain her side of the story and May could share her concerns. This simple act of talking things out could start to mend the rift between them.
A lot of fanfictions delve into Skye's love interests. Whether it's her relationship with Ward before his betrayal was revealed or potential new relationships with other characters in the show. There are also plotlines that involve Skye going on solo missions and facing challenges that were not shown in the original series, which helps to further develop her character.
Another plotline could involve the three of them facing an external threat together. Since Natasha and May are agents, they are bound to have enemies. Skye, with her hacking skills, could be a valuable asset in helping them defeat the bad guys. This adventure could strengthen their bond as a family. They might also face some moral dilemmas during this, which could further develop their characters.
I'm not sure exactly what you're asking about this specific fanfic. It could be about a particular plotline, a relationship development between Skye and May in that episode. Maybe it's a fanfic that focuses on their teamwork or a conflict they face together.
One common theme is Skye's struggle with her powers while being hurt. For example, she might lose control of her powers because of the pain or trauma she's experiencing. Another theme could be her relationships with the other agents being tested when she's hurt. They might have to make difficult decisions to protect her or help her recover.
One possible fanfiction idea about Skye could be a 'what - if' scenario. What if Skye had joined a different organization instead of S.H.I.E.L.D.? How would her character develop differently? This could lead to a whole new set of adventures and relationships, perhaps even changing her moral compass depending on the nature of the new organization.
You can try fanfiction platforms like Archive of Our Own (AO3). There are a lot of fan-authors on there who write about Agents of Shield and might have stories where Skye gets hurt. Another option is FanFiction.net, but AO3 generally has a wider range of content and better tagging system to help you find exactly what you're looking for.
One possible plot could be that Skye and May are on a mission together. They encounter an unexpected enemy that challenges their skills and teamwork. Maybe they have to rely on each other's unique abilities to get out of a tough situation.
Perhaps a fanfiction could be about Skye's pregnancy during a time of crisis in the Agents of Shield world. The team is dealing with a major threat, and Skye has to balance her pregnancy and her duties. She could be a symbol of hope for the future, with her unborn child representing a new beginning, even as they face great danger.
A favorite plotline is when Miles discovers a dark secret about his past that causes him great emotional pain. In some fanfics, this leads to him questioning his identity and his place in the Agents of Shield world. It's a complex and interesting exploration of his character.