Not bad. You really go into detail with your characters, despite your having a lot of them. While some places could use a little touching up (for instance, the vocabulary in some early chapters leaves a lot to be desired), your story shows promise. Keep it up...

This review is also coming to you from the Review Game's Review Marathon! Link in my profile.

The titles for the books the FBI had were...a bit too commercial in a way? I mean, FBI for Dummies? Really? :/ It gives me the impression not even they are taking their job seriously. This young female agent doesn't come off as particularly likable either. She is thinking blah blah blah when her supervisor is talking, despite her rank being very low. Just very little respect for no apparent reason (from what I see).

On the positive side - this chapter is far, far better than the first one. Overall, it seems a bit more mature than the 1st chapter and the setting is also interesting, plus we have intrigue fairly quickly (finding a potential suspect). But mainly - things are happening, and they are relevant to the story. First chapter really wasn't. My suggestion: Have this chapter as the first chapter. Just skip the prologue and character profiles altogether.

"The words carried along the waves of the noise."
What does this mean? Speaking the words IS noise. Which basically means you said "The sound was carried along the soundwaves" more or less...which is a bit of a major "duh", unless I misunderstood something here.

"‘Freak?’ How dare he, a total stranger, ** off at the FBI for whatever reason, call her a ‘freak!’ "
...Quite an immature reaction. He is shooting at her, but she gets ** off because he might have called her a freak? It doesn't make much sense.

Frac

Coming at you from the Review Game's Review Marathon (link on profile) which is dedicated to help spread the review love all over FP. To the review!

First thing first: The mini character profiles? Ditch them. All of them. Why? Because they are not a story, they are not a part of the story. These things we should learn by you showing us through the story, not just state and "get it over with" at the start. Needless to say, I read only two before skipping. It didn't catch my attention, and be careful about those things. First chapters are important.

"Yes, all little boys and girls should have been at home asleep in their beds. Most little boys and girls."
Second sentence is like a fragment. Try "Most little boys and girls were."

"“Say wha?” Arcus."
I think you're missing a "said" before Arcus or something, because it doesn't make much sense as it is...

"could be Agile-Super-Gymnast like Aeneas"
Suggestion: could be *an* Agile etc

"Rush of wind. Fast. Like a sudden inhalation of air."
I don't particularly like this line. Your sentences are for the most part regularly long. To have fragments all of a sudden works against you more than anything. This is not a narrative that particularly suits fragments either.
I'd just go with short sentences instead of fragments.

"“Now what?” Arcus frowned as if his friend had just spoken Martian. “Now what? I’ll tell you now what, Mr. Now-What. Now, what we do—is summon the Great Spirit from Beyond! That’s now what, so not another ‘now what’ out of you!”
“Oh,” both Aeneas and Achilles said immediately."
This dialog part is:
a) a prime example of "As you know Bob" (which means characters tell obvious things to each other in order to give info the reader). This is generally bad
b) The dialog itself...aren't these guys? The dialog has so far felt very "girly". Perhaps a bad word choice, but it just doesn't feel like these words are coming out of the male gender. If I hadn't been told they were guys, I wouldn't have guessed it. Very snappy and sassy sort. The whole "oo" and "Mr Who" in the cited dialog above are examples.

I can't say this prologe is successful. I think it drags on for too long with nothing really happening. Having a prologue should be an exception rather than the rule, and the exception is only legit if it is absolutely necessary to know.
And what I mean it say is: we did not know how the superhero school came into existence. It could have easily been retold through the school's history lesson or something of the likes.

I am sorry if I sound harsh. I do not mean to be hostile, just to offer concrit and help you improve.

Frac

good beginning, now follow up with something great