I'd like to talk about DISPEL, what we know of it, and what we think of it, and what its fate should be.

Bring out the quotes:

"Right now, all of you are in the headquarters for a special division of the FBI, one in charge of handling and concealing earthly supernaturals from public knowledge. We are known as the Supernatural Prevention Team, but we prefer to call ourselves DISPEL."

...

"To put it bluntly, magic is too powerful," Agent Gnome replied, "Ever since the dawn of time, it has been a force that can warp reality and the very world as we know it. Imagine if that kind of power fell into the hands more power-hungry individuals, or even a child who doesn't understand just how much power they possess alone."

...

Agent Gnome continued, "While it is true only people with the blood of the first witches in them may use magic to manipulate nature and everything associated with it, other spells like the transformation ritual can be used by anyone that possesses chi. Even with transformations alone, that power is still deemed too great to be used by anyone.

"This agency was devised to hide the presence of true magic in the world, so no one could use this power, either responsibly or irresponsibly." The man glanced from face to face of everyone before him, "The only ones who know about this agency are our own agents and a select, trusted few higher up in the government. Not even our current presidents knows of this agency's existence while we work under the name of the FBI."

And from the epilogue:

After the whole continent had been ponified, life had gotten interesting. At first it seemed as if mass panic was about to overrun every country in North America, but fortunately DISPEL had come forward to explain and take the blame. It had been decided that Taharis, who had been promptly imprisoned, would be pushed out of the picture for his safety, and locked away for life, just so nobody would come trying to murder him for causing this widespread ponification. (it was a wonder he wasn't given a death sentence) Thankfully, after days worth of explanations, most things began to calm down some. Of course, not everybody liked being turned into ponies, and a lot of people demanded that DISPEL use the Archterra to reverse the ritual. However, that was impossible for the agency.

Part of the reason DISPEL came forward was that this continent wide transformation mimicked the effects of Taharis' glove, using everyone's own chi to fuel the transformation. Now that everyone in North America was unable to use rituals anymore, DISPEL found it safe to let the knowledge of its existence into the open. But even then, the only way to reverse the transformation on everybody would be to use the Archterra again. But the alter had disappeared.

Apparently the whole land was 'transformed' in a way as well by 'The Ponifying', as some people called it. The clouds seemed to have stopped, only able to move over North America under pegasi power, rainbows had become actual liquid cascading from clouds, and animals seemed to have grown a bit more intelligent as well. Not to mention, plants with mystical properties began sprouting across the continent. It was like the continent itself had become like Equestria. I was just hoping I wouldn't find Poison Joke growing in my backyard anytime soon.

But, as DISPEL had explained, because of this change, the Heart of the Continent, the Archterra, had moved to another place. And with hundreds of thousands of square miles to scour for it below ground, it would probably take centuries to find it again unless we got lucky.

However, that all went down in the first week.

There are two things I'd like to discuss regarding DISPEL.

1) The President of the United States has for several presidents not briefed on their existence or purpose. Unknown if any past presidents were ever briefed.

2) DISPEL relied heavily on Security through Obscurity, and 'The Ponifying' is partly a result of improper security measures being taken to protect assets. To put it another way, it would be like gaining access to a place that could fire nuclear weapons with minimal protections, merely because it's location is supposed to be secret.

In regards to both 1 and 2, they are related. Because it was kept such a secret, modern security measures were unable to be taken or tested against other magic users. But more importantly, for such dangerous assets to be trusted with those 'higher up in the government', but not The President Of The United States, I would call treasonous. A violation of the oaths of office for service the Federal Bureau of Investigation, which it claims to be a sub-section of.

It also has implications of those 'in the know' having control over assets that are not what is considered the top level of government. In short, a shadow government hidden within.

I would expect the organization would cease to exist and those in control of it prosecuted for their part of the conspiracy.

4794168 I'm not gonna pretend I know much about how the FBI and such agencies should work, but 'secret organizations within organizations that the president doesn't know about' is a common thing in fiction. So it could have been a didn't do the research thing. Or maybe they operated under a dummy cover, the department that dealt with investigating and disarming the radical new age cult type stuff while going after real threats.

But I also should point out that their facility didn't lack modern measures. There were automatic security doors and such installed, but the facility was more a keep out/keep in, and Taharis was already in...

Either way, I expect they were largely, if not totally dissolved. And if they weren't, total change of leadership.

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4794168
I'd like to think that the Organization would have a massive amount of it dissolved and have the higher ups that worked in DISPEL locked away for Treason. I say mostly dissolved, because I think the president would use the remainder to instead of simply hide away magic, investigate magic related crimes and threats.

They are the ones who have the most experience in dealing with magic users and detaining them, and once the ones who were a bit warped in the wrong direction are weeded out (the probable majority), the remainder could work as a legitimate branch of the FBI instead of that shadow cell bull. Now, I'm not saying that people/ponies will just trust the group right off the bat, but they would have a chance at becoming something better then how they were. They would also have to bring in new people to fill the required number of people to work like that and be useful in more then one location, thus giving them a little bit of trust back quicker then normal.

That, and it'd be a great plot for a story.
NCIS, Law & Order, and Blue Bloods. Pony edition.

4794687 Gang of earth ponies committing a swath of ATM thefts?

They might also be good for training people on what outlook to keep in preparation for dealing with the newly magic magical world.