WARNING: As a precaution, some of the material mentioned may or may not be appropriate for all ages.

A Case of Trauma

If you were to just scrape the surface of the episode, as most people tend to do, you would have been given the impression that Ivy had dumped Brock.   After all, Misty kept repeating that, and considering his past luck with women it would seem like the automatic choice, but there are several things to consider.  One important thing is that, even among the women that Brock arguably adored just as much as Ivy (ahem, Florinda, anyone?), he never reacted as traumatized as he did in this episode.  What was noticeably different this time was the intense changing of atmosphere.  If you watch it again, you'll notice that the mood of the scene where he first reacts at hearing "Professor Ivy" mentioned is very serious, and not the same level as his usual depressed scenes.  Whereas other scenes would have some slightly comical music in the background, this scene had a very dark, sparse piece of music that gave you a feeling that whatever happened to him wasn't a normal event.   Even his voice quality gives this fact away.  His tones are very pained, but not as exaggerated as they can tend to be, and when he says he's not all right, you KNOW there's something wrong. 

From collecting feedback and re-viewing the episode, my honest conclusion to the question of "what happened to Brock" is that Ivy must have taken advantage of him in some way.  Now this can range anywhere from almost being forced to do "something" (and I'll be vague on that for your own imaginations) against his will, or, to put it bluntly, being raped, but Ivy most definitely did something that wasn't kosher.  Much of the time, victims of sexual assault have been known to try and run away from and/or deny what happened, not wanting to (or fearing to) discuss it even among close friends and family.  Considering this kind of response among "real life" victims, Brock's blue, tortured reaction easily fits into the victim category.  Presumably, he ran from Valencia Island after the incident, trying to get back to Pewter City.  Remember, Pewter City isn't far from Pallet, and from verging on starvation (I mean, look at his gaunt face in Ash's mother's flashback!), he wandered deliriously into a field that was close to Pallet, and was rescued (er, eventually) by Ash's mother and allowed to stay there.
So, instead of Misty's ill-conceived notion, what we have here is actually a tale of a traumatized young man who ran from his sexual assailant.

Evidence of the Crime

Ok, after reading the theory, I'm sure several of you somewhere are wondering just how I could possibly back this up.  The following are several of the more obvious arguments and the answers that help back up my claim.

A1: Misty said that Brock was dumped.
Well, frankly Misty could say the sky was falling repeatedly and couldn't be more wrong.  What you have to remember is that Misty, like Ash, is a superficial person.   That's practically written into her character.  She sees what she views on the surface to be the truth and rarely goes deeper to investigate.   She has done this on various occasions, one such example being her relations to Psyduck (boy, if that isn't superficiality, I have no idea what is).  Not to bash Misty, but the only person she's an expert on is herself.  Her basic view when she saw Brock in his traumatic state was "oh, Brock's acting odd, so therefore it's because of being dumped."  She has already taunted him before about being dumped by girls, and so this is of course an instinctive thing for her to say.  She's a very falliable character, and thus her comments are just that, comments.  If the narrator had said Brock had been dumped, that's one thing (even then, it could be questioned if the narrator was guessing or not), but what we have here is a young scantily clad girl playing guessing games with what happened in someone else's life.  Unfortunately, what Misty doesn't know could easily fill a Pokemon Stadium.  As people have probably learned, relying on what Misty says is about the same as trusting Ash's judgement in most things.   The bottom line-- take what she says with the smallest grain of salt imaginable.

A2: Meowth told Brock he "probably did something to embarass himself in front of Professor Ivy," and Brock did the same reaction.
Ah, here's the part that everyone probably thinks is the golden piece of proof, but it's just the opposite.  At first glance, Brock does indeed react to Meowth's statement, but if you listen closely, the key is in WHAT he reacts to.  If you re-watch the scene again, notice that Brock's head perks up and makes those blue-lined exclamations right when Meowth says the words "Professor Ivy."  Then, when Brock is making his traumatized pose on the highwire with the parasol, his words are "that NAME..."  When you actually examine what's being said, it's clear that Brock isn't  reacting to the "embarassment" Meowth refers to, but Professor Ivy's name instead.  So, actually, he probably wasn't paying attention much to Meowth prior to the mention of Ivy's name.  Brock reacts in this very same way in the ENTIRE episode to everyone else's questions-- he only reacts to her name, the name which reminds him of his own victimization.

A3: This is a kid's show.  It focuses on happy topics, not serious stuff like abuse and rape!
Well, for the most part, that is true, but Pokemon is a very curious show, in that a lot of things that aren't thoroughly discussed are actually very real issues.  For one example, we could take a look at the issue of dysfunctional families.  I doubt that people would ever think that a "kiddy" show would contain such things as a young single mother who was impregnated at 19 (or very possibly younger) by a man who ran out on her, or a deadbeat father who abandoned his entire family and, in the japanese version, a mother who did the same.  There are many "ugly" issues that would obviously never reach the surface for easy observation because, frankly, it would bother someone and then create controversy.  So, by hiding it and, in Brock's case, never discussing it (Ash: "I guess we'll never know what happened.."), the issues remain unresolved, but at the same time it gives the plot a complexity that would be otherwise lacking.

Hopefully, by this point, you've started to come around to my theory, and I'm sure some of you had a very similar theory before you even glanced at this page.   In short, Brock has been through love-and-loss experiences many times over, and seeing him in this sort of really rare agony is something that just makes you sit back and say "whoa...".  It's clear what happened wasn't your run-of-the-mill event, but hopefully, for Brock's sake, he won't be victimized to this terrible magnitude ever again.

... And as for Ivy, I hope they throw the book at her for this one.   Or at the very least throw her to James' Victrebell.