So, everyone, we're almost finished with Michael's backstory in Book 2, Part 1. Like I said, this part will focus on the story of Michael Wilson and his father, Edward Wilson. After Michael gets sealed, the focus will shift to his father, Edward Wilson, who will create the Agents of S.H.I.E.L.D. I'll also add Natasha Romanoff and other S.H.I.E.L.D. members because, let's face it, New York has many kinds of enemies and villains. I envision a world where Spider-Man can't protect every corner of New York alone, so S.H.I.E.L.D. is necessary to protect the other parts of the city. By the way, there will be appearances of Wolverine or mutants like Professor X and Magneto, etc., in Book 2. Also, Peter Parker will appear in Book 2, Part 2, his role will be similar to Miles Morales in the Insomniac game Spider Man 1.
By the way S.H.I.E.L.D wouldn't interfere the plot that much , they are more like just sidelines. Afterall they are too busy in another side of New York. So they just leave it all to Spider-Man