If you want to start writing 'prototype fanfiction', the first step is to immerse yourself in the 'Prototype' world. Read up on all the lore, study the different abilities of the characters, and analyze the various story arcs. Once you have a good grasp of it, think about what you want to add to this world. Maybe you want to explore a character's backstory that wasn't fully developed in the original. Or perhaps you have a new take on the power dynamics in the 'Prototype' universe. Start with a simple idea and build on it. As you write, keep in mind the tone and style of the original 'Prototype' works, but also don't be afraid to inject your own personality into the story. You can also look at other 'prototype fanfiction' works for inspiration, but make sure to make your story distinct.
First, get to know the 'Prototype' universe really well. Play the game, watch any related media. Then, pick a character or concept you're interested in. For example, if you like the idea of the super - powers in 'Prototype', you could start a story around that. Just start writing and let your imagination run wild.