Simon emails Blue and promises he won't push Blue to reveal himself before he's ready, but he thinks it's weird that Blue knows Simon's "superhero identity," and Simon doesn't know his. Blue's response is short and says he's happy that things are working out for Simon the way that Simon wanted them to, which confuses Simon. He emails that he has no idea what Blue is talking about. Simon writes that he hates that things are different now; even if Blue isn't attracted to him anymore now that he knows who Simon is, they still feel like best friends. Simon asks if they can pretend this never happened and go back to normal.
Since Simon wrongly thought Blue was Cal—and because Cal is now showing interest in him—Blue probably feels that Simon wanted Cal all along. This shows both Simon and Blue making assumptions about the other, and the consequences here are that the assumptions are fundamentally altering the terms of their friendship.