This is partially to remind myself and partially to open it up in case anyone else has any ideas:

The adversary has deliberately caused the raider plague, which spreads geometrically. He has a control mechanism in mind but it's not ready yet.

But what is it? I need to come up with something which is his plan for controlling the plague so that it does not get out of hand and destroy everything. The zebra antagonist knows this is important.

He might be thinking that once he has Nyx under his control that he can use her to just kill off all the raiders, thus stopping the plague. Or that Nyx would be motivated to end the plague on her own if she were powerful enough.

I know that he will use some sort of custom talisman which puts nearby raiders into a sort of trance, so that they don't attack him. This allows him to come directly into raider nests and take their captives for his own purposes.

I also know that ultimately, the raiders will be defeated by a megaspell detonation which "immunizes" all unaffected ponies so that the plague can no longer spread. It then becomes a matter of cleaning up existing raiders, which is a war they can win as long as there aren't new nests cropping up all over.

The main thing missing is the bad guy's planned method of controlling the plague. It seems rather risky to depend on Nyx converting into super-alicorn in order to stop the plague.

Maybe his solution is a preventative cure like what they end up using, but the plan would have been to immunize all the ponies by some sort of distributed vaccine, rather than the megaspell. Maybe the megaspell was just how it ended up going. Maybe he will put money into curing the plague in such a way that it leaves the zebras still vulnerable to it. I could see the bad guy doing that. This would need to be his own independent research team though, rather than using Fluttershy's ministry, because he can't reveal that he already knew about this plague. Maybe that game changes once he realizes that the MoP already has a sample anyway.

Well, this wouldn't be the first time an antagonist's plan hinged on a Deus Ex.

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Well, that's why I'm hoping to plan give him some mechanism that is planned in advance. Even if it doesn't work, it would be kind of stupid for him to go into this unleashing a plague on all Equestria without at least a plausible plan on how to stop it.

What about a kill-switch?

Not sure if you're still interested in the idea of a raider 'nest' being controlled / led by a single, more powerful individual, but tying into the idea of a talisman to gain control of the raiders, perhaps his solution is simply the ability to kill everyone infected? As opposed to healing /immunisation that is.

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That could work, but it's still limited in scope. How does one stop something which spreads on its own when you are just one individual? Also working that into the psychological aspects of the neurotoxin might be difficult. Currently I've got the raiders not attacking their own because they can "sense" other raiders similar to the whole zombie phenomenon every zombie movie seems to have where they don't attack their own. In this case, his talisman has two effects: it makes him "smell" like a raider, keeping others off his back, and second, it puts them in a sort of trance (not sure how this might work) where he can come in and take what he needs (their memories, and their captives) and leave without a fuss.

That's the "harvesting" aspect if his plan. But I still don't have a good "stop the plague entirely" plan for him.

Ok in my notes I found a mention of the adversary's assistant using the Black Book and zebra blood magic to link the talisman to the raiders. This gives me a whole lot of narrative flexibility to solve this problem.

It's worth noting that if this was his plan all along though, it was quite a gamble because he did not possess the Black Book when he unleashed the plague.

I still don't have a solid means for him to stop the plague. Part of the problem is that this is a zebra plague and our bad guy doesn't have a sample to work with.

So how can he claim to be able to control the plague if he has no means to do it?

About the only believable thing I can think of at the moment is that he is banking on the fact that he will succeed with Nyx and have his superweapon which he can then use to clean up the raiders when he takes over the world. If that is his plan all along, then it wouldn't matter to him that the plague spreads uncontrolled for a few months.

Of course, he wouldn't be telling Razor about this because Razor thinks this is all about torturing and killing Nyx not knowing that she would leave behind a powerful weapon.

Perhaps there might be something in the Black Book? The Black Book might have been what originally created the parasites in the first place as a weapon and so has a necromantic spell or potion that renders the user immune to the parasites effects?

Our villain gets the black book at the opening of chapter 7. However, the book will surely provide some useful things for him.

So here's the idea currently (subject to change).

M.A.S. will have a bioweapons division which specializes in genetic engineering. It's a startup division and will receiving funding from the Nobles in exchange for an empty promise that Luna will be removed from power. I have no details (yet) as to what this promise looks like, but that can wait until later.

The bioweapons division will experiment on parasprites to make them seek out and eat the plague bugs which are the cause of the plague. These customized parasprites can only eat the bugs, and they can seek them out accurately within a limited range. They also will die off if they can't find something to eat within a short period of time. They will also be very small. About the size of a fly.

The idea of using this as a control mechanism is that if a single modified parasprite is released near a nest, it will fly off and start eating, multiplying as it goes. The parasprites would be quite annoying to the infected, biting at them but not in a dangerous way. Since the infected do not feel pain anyway, it's more of an annoying distraction than anything. The parasprites would be effective at sterilizing a nest, making it no longer a threat of spreading the plague. Note that it would not cure the infected though, so they would still be a threat in terms of their usual infected pony behavior and have to be dealt with. Fortunately, they are not particularly skilled fighters and are mostly a threat to civilians. I do not plan on there being any sort of "cure" for their condition. Unlike modern tv shows, I don't like "reset button cures". The infected have extreme nervous system damage, so they'd be stuck in that state.

So if this is the mechanism our villain claims to be working on, he just needs a sample plague bug in order to "program" his modified parasprites to eat. He doesn't have this yet, but he is confident that once the plague starts spreading, it won't be too hard to get a sample. Meanwhile, he could be having a team of researchers working on the parasprite modifications while he waits for this.

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I know we talked today about the whole "audio based paralysis" weapon for Storm to acquire and then use that to harvest the memories.

But I think this may be better. Most of the discussion above this point in the thread is old and obsolete apart from the final post. So I'll be expanding on that idea and refining it to serve a dual purpose.

The main change is that these modified parasprites will be designed to have a short-term paralysis on whoever gets bitten. Bio engineering is the name of the game here. It can be designed in advance as Storm's "mostly finished" control mechanism which serves two purposes. The parasprites will eat the plague bugs, but they will also bite the infected ponies (in the effort of getting at the plague bugs) and inject them with a temporary paralysis venom. After a few minutes, they fall over and can't move. After a couple hours, it wears off.

So the idea here is that Storm (and probably Caraway) will sneak into an area where the infected ponies are. They stay far enough away to not get attacked, and release one of these very small parasprites. It flies off and starts eating the plague bugs off the infected ponies, multiplying instantly as parasprites tend to do. After a few minutes, the infected ponies start dropping. When it's safe, Storm and Caraway are free to collect memories and get out before the effects wear off.

As of chapter fifteen, when Storm meets with Razor, he's got these modified parasprites designed already. The only missing ingredient is a live sample of the plague bug, which Razor will fetch for him in about 24 hours.

That's probably as simple as I can make it.