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.
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.
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.
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.
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.
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.
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.
Skye's character has a lot of potential for development in fanfiction. Her journey from a hacker to an agent is full of twists. Fanfiction could focus on her training, like how she masters combat skills and espionage techniques. It could also show her dealing with the pressure of being part of S.H.I.E.L.D.
One plot suggestion is that Skye's pregnancy is part of a prophecy in the Agents of Shield universe. The baby is destined for great things, but there are those who want to stop it from being born. Skye and the team must fight to protect her pregnancy and ensure the baby's safe arrival. Along the way, Skye discovers more about her own past and how it relates to the baby's future.
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.
Skye would probably be cautious at first. She doesn't trust easily, especially when it comes to people who might be on the wrong side of the law. But she's also curious, so she would be interested in what the hackers have to offer in terms of knowledge and information.