I hope you don't mind, but I'll be writing my thoughts in list format as I'm reading through this.
1. First and foremost, I can tell you're writing this in Word, which is good. What's bad is that I can tell because you have that random line of commands at the top of your post that defines what font set you're using. If you see that pop up, remember to edit it out.
2. You have random capitalization here and there. For example, I'm pretty sure "wash" shouldn't be capitalized because it's not a proper noun. Rather, it's just a term for a type of Magma grunt (which also isn't capitalized). Moreover, "headquarters" should not be capitalized either, and you never capitalize a letter in the middle of a word (like in WashingMachine – which should be "Washing Machine" anyway, but hey).
2a. However, you should capitalize proper nouns, as in the case of Washing Room, a particular room in Team Magma's headquarters. (Or, for that matter, Team Aqua.)
3. You keep using "unaffiliated individual" (or some variant thereof – remember to spell check your work before posting). It might be better to just say "intruder" because this packs more punch and makes it clear that this is an uninvited guest, rather than, say, a potential voluntary recruit.
In general, don't resort to a thesaurus to figure out how to phrase things. From what we can tell, your narrator is a grunt, and grunts' vocabulary isn't necessarily erudite or overly flowery. While you used words correctly (more or less), saying things like "he capitulated to the cattle prod" sounds over-the-top and pretentious.
4. Moreover, description. There's a bare minimum of it here when you could very well have a lot of it. For example, rather than describing this intruder as surrendering to the cattle prod seems vague and less powerful than letting the reader see him scream every time the cattle prod touched him until he begged for mercy. There's also no dialogue, so we can't actually read this grunt snapping at the intruder to get up or the intruder relenting desperately. It's more or less a summary of what's going on, rather than something that would let us visualize this struggle. As a result, this chapter doesn't seem as powerful as it can be, considering how dramatic dragging a victim to a brainwashing room should be anyway. Remember that the reader isn't psychic, so we can't tap into your head and get from it the mental images you want us to see. Therefore, you really have to make an effort to deliver that for us.
5. Whenever you use a colon ( : ), replace it with a period first to see if you end up with more than one complete sentence. If you do, keep the period in. If you don't, keep the colon in. There's exceptions to this rule, of course: if you can replace the colon with the phrase "that is" (in the sense of "to be more specific"), then it can serve as a means of joining two sentences together in a compound. However, in the case that you're using it within this chapter, you'd end up with a run-on, so you might as well just split "When Team Magma had selected me to be a grunt in their ranks…" into a separate sentence.
6. You'll really want to remember to proofread and spell check your work before posting. If you don't want to run through all the correctly spelled words (read: any Pokémon name) during a run-through, turn on spell check as you type (Tools > Options > Spelling & Grammar in Word 2003; File > Options > Proofing in Word 2010) to get red squiggles under each misspelled word. That will help you pinpoint all words that the dictionary doesn't recognize without having to go through the entire document.
Yes, it's a good idea to proofread and spell check before posting. At the risk of recycling analogies, think of your writing as a road. A mistake here or there might be a bump or crack, but a lot of mistakes creates a road that the reader won't enjoy driving down. Smoothing out the metaphorical pavement by removing as many mistakes as you can will help them focus on everything around the road instead of on the road itself.
7. Remember that period test I mentioned in point #5? It works for commas and conjunctions (and, but, or, for, nor, yet, so) too. Replace this kind of combination with a period to see if you get two complete sentences as a result. If you do, leave the comma in. If you don't, take it out. I say this because the comma after "Aqua" is unnecessary; this isn't a compound sentence.
8. I have to smirk at the idea of naming a character Nettle, but this is just my egotism talking.
Overall, I'd hate to say this, but there's just not much here. You have an interesting concept (so far as having a story told by a Magma grunt in a distant future – but see below for everything else), but there's a lot of errors here that make me think you'll want to slow down, take your time, and most of all, proofread. There's no dialogue here, no description, nothing that would help us envision what either the grunt or the intruder (or both, really) are going through, but this should be a very dramatic scene.
I mean, a prisoner is getting dragged into a room (possibly literally, depending on how fond of the cattle prod our narrator is or how resistant the captive is at first) to be brainwashed, so naturally, you'll want some dialogue and a lot of description. Let us hear the intruder's screams. Show us him struggling either to fight back or to keep himself from breaking under the cattle prod. Tell us about how the cattle prod feels in the narrator's hand or what smells he catches after each use of it on the prisoner. Give us a good idea of what the Washing Machine looks like to drop hints of how painful this process is. Be detailed enough to help us get a clear picture of what's going on so we can cringe at how twisted this is. Otherwise, it's just a summary of what's going on, and that just won't be a particularly effective first chapter.
Now, as for the concept. I didn't get a chance to comment in the Plot Bunny Thread, so I'll offer up my issues here. There's three problems you'll want to think about when writing this.
1. Team Magma was not after the eradication of all Pokémon on Earth. Rather, they were for the opposite: expanding the land to allow all life on Earth to thrive a little more. They just had stupid ways of going about it.
They were also not after world domination, either. A lot of authors make the mistake of thinking every evil team is after the same goals as Team Rocket, but really, Team Magma were just ecoterrorists. Once they got what they wanted (expansion of land), they probably wouldn't bother maintaining their activities. After all, it's the land that interests them, not the ability to rule it.
2. While I can accept that this is an AU, it's worth noting that the moment Team Magma awakened Groudon and nearly got what they wanted, Maxie (Magma's leader) realized immediately that the actions of his organization would destroy the world. As a result, he decided to drop his plans, stop being an evil jerk, and work to clean up the mess Team Magma created. In other words, if Magma followed Maxie's orders, they would have actually turned into good guys by the end of the games, not complete monsters.
3. The ecosystem. Astinus touched on this in the Plot Bunny Thread, but I'd like to clarify with an example. Think about insects. Common insects found everywhere. You don't really pay too much attention to them, right? Now, think about what would happen if every insect in the world died off all at the same time. Suddenly, the decomposition process would take a lot longer to achieve (because flies help break down things into nutrients for the soil), pollination just wouldn't happen (because insects are huge pollinators), and the food chain would lose one of its most basic links. As a result, you'll have dead matter everywhere, plants would die off, and so would animals.
The same thing would happen if every Pokémon simultaneously disappeared. Pokémon aren't just pillars of society. They're also major elements in that planet's ecosystem. (Some even embody forces of nature themselves, depending on what canon you're using.) To remove such a major part of that world is risking the extinction of everything on that planet. Sure, you've got Orre, a region without Pokémon, but you'll also want to note two things. First, it's the only region that doesn't have Pokémon (and even then, that's not true in XD). Second, it's kinda a wasteland. Nothing but desert as far as the eye can see. Without imports, this kind of place wouldn't be a nice place to live.
Of course, you've also got to think about the fact that, as Astinus noted, Pokémon are major pillars of society. Without Pokémon, it's very likely that humankind wouldn't know what to do with themselves. Also note that if the entirety of the organization had only four Pokémon, every grunt would probably need to adjust to the loss of their Pokémon. And then we'd have to assume that this wouldn't somehow result in a coup.
In short, I guess you could say I think this just needs a bit more thought and time.
Good luck.