Hugo said:
I also have to choose whether the PCs are normal people who get caught up in a massive shadow invasion, or if they work for Dept 7 for the government. If they were normal people the shadow invasion would have to be on a much larger scale, they would be trying to survive as the world collapsed and a large portion of it's population was destroyed. As normal people they wouldn't be able to just get an m16 to kill the zombies, this could make things interesting. Any input is greatly appreciated.
Speaking from experience, let them be normal people: it makes things a lot more interesting. Assuming you are talking about a complete or near-complete collapse of society, the first issue with normals will be how they try to protect their loved ones. If they are immersive roleplayers, that will likely be an all-consuming task for a while unless you either eliminate all of their loved ones in the initial game-start (which will probably leave them all with a fatalistic "punisher" mindset) or you provide a safe faven for their loved ones ("you guys stay here in the hidden shelter while we go for supplies") which gives a nice "everyone is depending on us" tone, or you can leave it to them to develop on their own.
Aside from the "loved ones" issue, the normal-people cast is great for rewarding ingenuity. The most realistic response from normals might initially seem like total power-gaming, but that can be a good thing. What I mean here is, yes, given a zombie-world-collapse situation, wise people are going to find the closest army depot/police station/gun shop/demolitions supplyhouse and stock up on whatever they can get. After that, they will probably look for chainsaws, molotov cocktails, and nail guns if they have to. Just trying to sneak into the armory can be a great adventure if done well.
From an over-arching plot standpoint using normals as PCs, you can have a ton of stuff laid out for you with very little work:
Maybe you start with the initial X-files weirdness like one or two stary zombies or just a zombie-alligator in the sewers type thing, maybe enough for the PCs to get a hint of what is coming and deal with something small on their own, and maybe they even think they can keep the whole thing secret. But when the weirdness hits the evening news, they know they are not in for that kind of quiet-conspiracy situation. Then the weirdness/zombie attacks start getting reported all over the planet, and chaos ensures. An adventure centered on rioting in the town, maybe, or the PCs try to prevent a local outbreak, while you present total destruction on the news elsewhere. As civilization collapses elsewhere, news reports from the outside world are cut off. You can have the army step in for a brief period before getting overrun. The power shuts off one day, and the water a few days after that, while a lot of people leave town to "hide in the hills". You can give the PC's a lot of options at that point such as to stay and fight what is coming or head for the hills. Either way, you can have a good adventure when the big zombie invasion finally hits. Then after that, you have the fun of getting supplies for whoever is left, such as medicine, food, replacement parts for the radio transmitter, etc. A supply run through zombie territory would be a good mission at this point. Similarly, you can have the rescue mission in here, where maybe some friend of the PC's gets taken by zombies, or even kidnapped by a rogue military unit, or perhaps the. Anyhow, by now, the whole campaign is in a semi-stable mode where you have some number of people holed up in some secret community, surrounded by zombie-territory and cut off from the rest of the world, when you get a message. Somebody has an idea for how to beat the zombies, but somehow you have the get the secret weapon/formula/incantation from somewhere far off. So the PC's do the "quest" where they go on a long trek cross-country to get the goods. Add in as many adventures as you want along the way, and show off just how bad the destruction is elsewhere. Finally, the PC's get the goods (and head back home if you want) and they beat back the major zombie menace. At this point, the campaign can be over, or it can be a new start (because the solution/secret weapon only eliminated the zombies, not the various mutated shadow creatures that now lurk in the wilderness, so life is somewhat safer, but you still are not really safe outside your compound's walls.)
I think somewhere along the way I just stopped offering advice and my creative juices took over, but maybe some of that will be useful to you.
By the way, I would also definitely throw in an evil army unit or two, a competing compound with a tyrannical leader, political problems within the PC's compound, and a mysterious stranger who staggers into their camp with a cryptic warning before falling over dead.