Instead of trying to guess what the story would have lead to, I would, for a change, try another approach. I would try to guess what JMS might have imagined, what courses of action he could have foreseen for fighting the Shadow plague.
I would approach this question from the aspect of theoretical biology and nanotechnology. My knowledge of the possibilities of these sciences is limited, but I can imagine a bit. The following are all guesses.
1. What is the Shadow plague?
Most probably a swarm of nanomachines, built intricately enough to be considered artificial life. They feed on their environment to obtain energy, they reproduce to maintain their numbers and they mutate to find new ways of existing.
2. What is its purpose?
It does what the Shadows wanted. What would they want? I suspect that besides being a weapon, it is also a tool and an instrument of research.
It maps the strengths, weaknesses and peculiarities of an ecosystem. It learns how to exploit the system, how to change it and (if necessary) destroy it. As the experiments it undertakes are quite random, it causes some degree of destruction in its learning phase.
What will it do after reaching a critical mass of knowledge? There are many possibilities. I suspect that it listens for directions from its masters. As there are no Shadows around to direct it, it might choose the most primitive course and simply destroy.
Or it might randomly destabilize the ecosystem, create forced evolution. While doing this, it would still try to listen to the Shadows, to find out what they want to do with this planet.
3. How does it work?
The nanomachines extract energy and matter from their substrate. They learn to live by processing materials via chemical or even nuclear reactions. They learn to feed on living beings, either as symbiotes or parasites. Perhaps they even learn photosynthesis.
They evolve and spread at a greatly accelerated pace, eventually reaching every habitat. They also communicate with each other, exchanging "tips and tricks" for better survival and influence over the environment.
While doing this, they learn skills which the Shadows might want them to use.
4. How to cure it?
You can not make an ecosystem immune against such an advanced intruder. It must be stopped in one way or another. How?
4.A. Destroy it.
The principle is simple: like can fight like. Get a similar breed of nanomachines and let them fight, consume, oppose and resist the Shaodow-built ones. The Shadow plague will of course realize that it is being attacked.
How will it react? It may pull back to study its opponent, grow stronger from experience and overcome the attack. It may turn its attention away from the ecosystem and focus on the attacking machines/creatures. Damage to people, plants and animals might stop for a while. It might seem defeated while in fact, it is only learning to fight better. After defeating the cure, it would come back and be stronger.
4.B. Emulate a command from the Shadows.
It would be natural for them to want some influence over their creation. They would want the options of stopping or redirecting it. The additional programming would probably not come as a signal. It would be delivered as an new breed of nanomachines. Their structure and presence would tell the original intruders how to change their behaviour.
This approach has a rather tricky side: you would have to know exactly which command you are delivering. As there are no Shadows around to teach you, you might give the wrong command.
Instead of giving the command "sleep forever" you might give the command "sleep ten years, then destroy all sentient life". You might accidentally tell it to stop all volcanic activity, to get rid of oceans, to create an ice age, to make deserts become forests, to make people live 500 or 25 years... whatever.
To fight a Shaodow plague which the Drakh have simply dumped in good hope may be relatively easy. If it's a random agent of chaos, it may give enough time to study it. If the commands given by the Drakh were weak, it might be easy to neutralize them.
But to fight a Shadow plague which has gathered experience and then received a correct but destructive command may be much, much worse.
Giving the wrong command might too produce the effect of an apparent cure. The plague would refocus its efforts and cease bothering you for a while. Until it is ready to carry out its task. After it has become ready, everything would depend on the command. It might do nothing, great good or great harm.
[This message has been edited by Lennier (edited January 04, 2002).]