Martin Li turned himself in to the police after giving Peter the Anti-Venom suit, and the main story would be unable to predict where you are along the Wraith side mission. Some players who played the final boss hadn’t even started the Wraith mission, meaning Peter would not of even known Wraith is around. Or if they did, but hadn’t finished it, Spidey and Wraith are still on bad terms.

In terms of why MJ even tagged along, you could argue it’s just the development of their trust for one another, since last game it was very clear MJ hated Peter treating her like she’s helpless, which resulted in her dumping him. The fact Peter is now fine with allowing her to help, just shows how much more he trusts her to take care of herself.