One idea could be that the reader is a new adventurer in the Minecraft world and stumbles upon an Enderman who is different from the others. Instead of being hostile, it seems curious about the reader. Another could be a story where the reader has the ability to communicate with Endermen and tries to bridge the gap between them and the other mobs in the game. Or perhaps the reader gets trapped in the End dimension and an Enderman becomes their unlikely protector.
In an Enderman x Reader fanfiction, a good plot might be that the reader is a builder who creates elaborate structures. An Enderman is drawn to these structures and starts to watch the reader from afar. As time passes, the Enderman begins to leave gifts for the reader, like rare blocks from the End. Eventually, the reader notices the Enderman and tries to communicate with it. They could go on adventures together in the Minecraft world, exploring different biomes and facing challenges side by side.