Oh, I forgot to point out a couple of things. I'm not sure if you're doing it on purpose, but anyway.
First of all, I'm pretty sure that cubones and marowaks are not native to Lavender town. They're just buried there. This may be just me, but personally I think it would be more realistic for the mission to take place somewhere like the Safari Zone.
Also, you do remember that the Rockets were first encountered stealing fossils from Mt. Moon, right? :P
That's about it, I think
Hey, thanks for the comments, but actually, yep, it's all intentional. Cubone are native to Pokémon Tower; if you check the Wild Pokémon data for Pokémon Tower floors 3, 4, 5, and 6, wild Cubone can be found there. And if the Cubone were just buried and it's dead Cubone there, or the ghosts of Cubone, then there would be ghosts of all the kinds of Pokémon there, instead of Ghastly and Haunter. No, the Cubone are definitely alive. As to the one ghost Marowak, the game says that the ghost Marowak was killed by Team Rocket in the Tower defending its offspring Cubone from the Rockets. Besides, Team Rocket has a known presence in Pokémon Tower, so it makes more sense for them to be there early on than it does for them to be in the Safari Zone, where there's no canon game evidence that they've ever shown up. (Actually, I will be doing something minor with the Safari Zone later on, but it's not a big operation like their projects in and around Saffron.)
And yes, I know that Team Rocket is first encountered by Red (generic name for the original game hero) in Mt. Moon. :P That doesn't mean they were ONLY in Mt. Moon when Red ran into them, though. By the time Red beats Misty and tries to go into the north gate of Saffron City, Team Rocket has already completely taken the place over, since the guards won't let him in. Since taking over an entire city, especially one with such powerful trainers in it as Sabrina's trainers and the Fighting Dojo, must be really hard, odds are that Team Rocket has had a strong presence in the Celadon-Saffron-Lavender area since long before Red even got his first Pokémon. This is a Team Rocket game, but you aren't Jessie, James, and Meowth; you're not following the twerp from Pallet Town around from city to city, heh. News will reach the Saffron base that some strange kid made mincemeat of the Grunts in Mt. Moon about the time you get back from your first mission in Lavender Town, and you'll meet Red yourself fairly soon after that. Mt. Moon will come up again later on in the plot, too, though probably not in a way you'd expect.
