Keep asking your wife :)
Really though, that is your best option. You will always overlook things outsiders to the game will notice, simply because you might have an X number of ways of how the story could develop in your mind. So your best option is to work with someone who is outside the game and whose imaginations on things like that will not be limited by system rules and tropes.
UPDATE: Also, don't forget, you don't have to write down every single detail. Have the general plot in mind and then if your players give you something you haven't planned on, make it fit then and there. You'll be surprised by how many things the players will think of that you hadn't, so don't try and cover them all, do it on the fly.
Don't.
This is something I started to do in my campaigns. When the players derail the plot, I build a new one for them to follow. If they want to focus on how the bad guys have tech that isn't public knowledge, they can. They're ignoring the larger problem of "oh crap, zombies" while doing so, however, so simply let the rest of the world go on into decay as they mess around, until they're forced to confront the fact that the secrets being kept are perhaps a little less important than the fact that everything's collapsing around them. Let the plot equalize itself over time by letting the players do what they want; eventually they'll realize that they can expose this whole secret and conspiracy stuff, but don't have anyone left to expose it to because they've all become zombie food.
However, if you must.
Make them choose between their mission and the mission.
Eventually they have to be confronted with the following conundrum: Is our personal investigation getting in the way of the good of mankind/not being eaten by zombies? If they don't do this, then they'll continue their investigation as planned, but the world around them effectively ceases to exist as it was, meaning that they have to take responsibility for everyone dying and they no longer can get any help. If they're working with someone, have them pull support. Do so in a way that enhances the narrative, however "New York's almost overrun! Get back here or don't come back ever." works better than "and they didn't want you doing that.", because one sounds like a logical reason, and another sounds like railroading.
Dry up their leads.
If you really want them to stop searching for evidence, have the other corporation collapse. Their secrets and technology are gone with them as they crumble from within. The players could still try to investigate, but there aren't any real survivors to explain things, and anything they find essentially ends with "and now we're all gonna die".
Wave it away.
One thing it sounds like you're asking is how to explain the presence of high-tech gadgets. Simple; they're one-of-a-kind and untested. Sure they do what they're supposed to, but they're nowhere near finished. They're prototypes sent into the field. Ultimately, it's sort of your fault for introducing it if you can't explain it, but simply have it end. No more supertech gear because it didn't work, as the field trials showed. The only one got destroyed, beat up, or otherwise compromised and it proved to be less valuable than its investment.
Best Answer
Little By Little
I am, in fact, running a Dresden Files campaign right now. We're nearing the end of our third "book" - we've arranged the game in books and I've got some things I've learned that might be of use to you. But as the title says, the way to do what you want to do is little by little.
First of all, forget about plotting RPGs. The plot of a story is the list of all the things that happen. But you can't plot, because you can't predict what any of the main characters will do at any time. Which is great. Because you have a bunch of smart people (your players) taking care of that for you, so you can concentrate on other stuff! All you can do is provide instigating events for them to react to. In other words, you can't plot, but you can plan.
By the Book - how the system can help you:
The Dresden Files RPG has some great features built in that are going to make some of this easier. It's got a great city-creation system that will help you make sure you've got a city full of interesting factions and characters. And I don't know if you've played FATE-powered games before, but you're going to end up knowing a lot more about the PCs than how hard they can hit something.
Begin by Ending - how to get started:
If you wanted to drive across the county, you'd never try to predict exactly what you would do at every step. But you would want to know what city you intended to drive to before you started, right?
Before the game starts, I talk with my group about what we're going to be doing in general - I make sure that I'm not set on an all-Nevernever-smackdown game if the players are more interested in playing cat-and-mouse with mortal authorities while hunting Lawbreakers for the White Council. Once we're on the same general page, I would do the city and character creation. Then, I have a fantastic resource at hand: The PCs and the city. Those are like a mad scientist's control panel, full of buttons to push, levers to pull, and dials to twist. The players have just given you the keys to the characters. It's up to you to drive them! Pick a big bad that will push those buttons - activating he Aspects of characters and city alike.
Now, jump to the end. Decide what would happen if the PCs weren't there. What is the thing that your players are averting? Make sure it will make the PCs take notice. It doesn't have to be the end of the world, but it has to impact the PCs somehow. Take this consequence of inaction as an example:
Some groups may not think that's worth getting out of bed to prevent. But if your PCs all grew up poor in this city and have aspects to reflect it, this may provide plenty of motivation.
Usually, of course, the consequence of inaction is bigger.
for instance. But bigger isn't necessarily better. Harry Dresden goes to tremendous lengths to prevent small tragedies sometimes.
Once you have a Big Bad and a goal for him / her / it / them, you can try to see how the Big Bad's agenda coincides with or crosses the agendas of the PCs and the city factions you defined above. That will give you some insight into what could happen in the future - but you don't need to get it all pinned down yet. You know the endgame and the primary actor. That's enough for now.
It's also possible to have endgames that don't have actors - inexorable threats like asteroids are essentially timers for this endgame:
But villains are generally more interesting for you to play than forces of nature are. Asteroids don't cackle and tent their fingers.
One Bite at a Time - how to eat an elephant:
Here's how I handle planning a given episode: Take a notebook and make some columns on it with these headings: Who, Wants, So. Use a notebook. It helps keep you organized. Write longhand. It helps, I promise.
Now, take that notebook and write a name in the Who column. It can be your villain, a PC, a city faction, an NPC, or whatever. You might write "The Red Court" in your Who column.
Next, write down what they want in the Wants column. Wants should usually be short term - so the Red Court is going to put their puppet on the city council. Their want should be what they want next - like "The Red Court wants to get the councilman addicted to Red Court saliva."
Now that you know what they want, write down what they'll do as a consequence in the So column. They want to get the councilman addicted, so...."They arrange to have a fundraiser at a Red Court stronghold where they can get a little face time with the councilman."
Now you've got a strongly motivated action for the bad guys to take - repeat this until the "prods" for your upcoming game start to take shape, and then you're done with the "What's going to happen?" part of prep!
All you need then is to sketch out people and places you think will be important. Don't go nuts - you'll be wrong about some of them and don't want to waste the work. And a lot of games (and DFRPG in particular) make creating these things on fast and simple enough to accomplish on the fly. I just ran an awesome session with a rescue mission / fight in a burning, collapsing warehouse full of nasties that I built right there at the table while everyone else was grabbing a bathroom / soda break.
And that's it. By keeping this in a notebook, you can flip back a page or two and see if there are any loose ends from last time, or any previous time. If a couple of sessions back you said that
but you never got around to dealing with that, you've got yourself a nice loose end to pick up and tug on.
Here are the advantages I have found to using this method in my fairly long-running DFRPG game (and others before this):