Having started a game — you've set up your character and picked your Fort-to-be — you now have to make your way across the town of Piety to your base and remove any undead that might be inside in order to seize control and get down to the serious business of building up your Fort. It is important to note that the goal of Fort Zombie is to survive, which means finding weapons, ammo, food, supplies, and other survivors, all with the intent to survive the Big Wave of zombies coming your way. Shooting every zombie in sight, while fun, wastes ammo and usually just alerts more zombies to your location, so move quickly to your base and clean house there.
Once you've cleared out your base and had a look around — maybe picked a good choke point to build up around, eventually you'll need to get down to business. Click End Day. This will start the game clock, after which you have around a couple of weeks to get ready for the final battle. During that time, your time is split between two things.
How you balance these is up to you — both of them consume valuable time before the Big Fight. Night time is extremely dangerous, but you can opt to get in as many missions as you can before it comes. Judge your time poorly, and you may find yourself stuck outside after dark and running for home as if hell was on your heels. Which it will be.
Missions are when you hit the town looking for supplies, survivors, and weapons, while dodging the undead. Missions take place in a full 3D environment where certain interaction are handled as an RPG ( i.e. your ability to hit what you aim at, searching for hidden supplies, the speed at which you run, the height at which you jump, etc.).
You can choose to forgo missions, spending the day giving survivors orders and recuperating, by not taking on any missions and hitting End Day. Most likely, you will want to pick your missions carefully while spending some time back at base keeping the survivors on-task, before committing another day to the dust heap, bringing you one day closer to your Fort Zombie showdown.
When you've done all you can for the day, it's time to catch some sleep, and start the next day. Click End Day back in the fort to catch some well-deserved rest before you start the next big day.