You know, I did reply to your idea FourCartridge, but it got lost and I got pissed and I gave up. So now, I'm gonna re-type everything I said before because no one replied to your plot dilemma to begin with... And it'll be in a spoiler tag so that other people don't get spoilers too, I guess.
In canon, there are a few guns here and there with a few banned episodes, and one other episode aired in the first season. Afterwards, they're all a bunch of nets of uber Poke Balls or another. Hunter J did have a stone-gun-Medusa thing. So there isn't much else to add, except maybe alcohol burns or some gasoline and fire. But if you think about it, Pokemon would be resistant to most of that anyway since that would be like a Flamethrower.
The "what have I done" is a bit cliche, but if you can pull it off, good for you. And if someone shot you up beyond belief, would you forgive them for not killing you? This did happen in the Bourne Ultimatum, where Jason Bourne doesn't kill another agent dude because he thinks it's pointless, and the agent dude doesn't shoot him later on. But that's as far as it goes really. It would take time to forgive someone.
As for a sidekick... In the chapters you have written so far, Greg isn't really keen on Pokemon yet. You could develop that into him later on, so a sidekick could warm up to him. I don't think Keldeo would be willing to join him at all. First of all, he's a human. Second, he's the human that shot them up to oblivion. Third, they wrecked his car. There's nothing wrong with using a normal Pokemon, but be careful when you introduce it. You don't want to force it out of nowhere. A good idea could be some kind of Pokemon he meets in the towns, since he'd be a lot friendlier around people, if he thinks of them that way. There aren't many specifics to go by, but I guess one of the elemental monkeys could do the trick. Monkeys aren't that weird, the only problem is their odd coloring to Greg, but that'll grow off him. I think he could be more comfortable around them rather than, let's say, a Haxorus or a Beartic.
I'm wondering why Greg wouldn't like N, or like him. N represents how people abuse Pokemon, which is basically like PETA. Greg shoots up Pokemon, so he doesn't necessarily like them as of yet because of his previous experiences. So I don't see why Greg would particularly care if N is the leader of Team Plasma. The only people that would disagree with N would be Pokemon trainers/breeders/coordinators/etc. If anything, N would hate Greg for shooting at Pokemon and hitting them upside the head with a wrench. I don't even think Team Plasma would be completely relevant in this story. Greg shouldn't care about it, since his focus should be going back home, not on Pokemons' rights. I know you want to put N in as well as Team Plasma, so they could be more like Greg's saviors or something. In reality, Greg wants to see a professor. Maybe Professor Juniper, or a made-up Professor, so he can make a dimensional portal and go home.
You keep referring to the real world and how Ghetsis somehow got there, so I'm curious as to how they get there in the first place. And Ghetsis going to the real world is a bit odd. You could just make him die of disease or falling off a cliff or something. If you mount an invasion, there won't be much of Team Plasma left. N could be the main antagonist over Ghetsis because the main antagonist isn't the ruler of the organization. It's the protagonist's biggest enemy. And besides, N is the leader/king of Team Plasma.
Greg's belief would be about Truths and Ideals are needed, wouldn't it? I mean if you think about it, they depend on each other. Dwell between both, so to speak. This goes hand in hand with the battle. I guess N could have Kyurem instead. Or, Greg could have Kyurem and N one of the dragons.
I found this nifty quote, which is from a fan game.
You resonated with Kyurem- believing that Truth and Ideals must go hand-in-hand... you shunned Kyurems brothers, and instead chose him... but you are also a hypocrite. By choosing Kyurem you make people believe you will listen and accept their beliefs. Yet you come to stop me from doing what I believe without question.
But with this, the tone is shifted. You're not focusing on Greg going home. You're focusing on Greg and how he got drafted into the Truth vs Ideals war again. Staying in game canon should be easy because you nearly follow the whole thing. However, the tone is a bit tricky. You could focus more on the characters and how Greg really doesn't want to go home, he realized, because there really shouldn't be a way back unless Palkia did something.
Just a few random ideas. You don't have to use any of them. It could be that this is the exact opposite of what you want to do, and if that gives you ideas, then I did a good job!