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The game is organized into 7 days, with 3 missions per day. The 1st day's missions are always the same each time you start a new game. These are the only fixed missions; the other 6 days are randomly generated.
The 1st mission is simple. There are 2 enemy fighters at Nav 1, two more at Nav 2 and Nav 3, and 4 at Nav 4. It is difficult to complete this mission without taking at least some damage, but it is possible. Destroy as many of the enemy as you can, but don't worry if you have to skip a few because of damage.
The 2nd mission is a scouting mission. The goal here is recon, not kills. There are 2 fighters at Nav 1, and more fighters at Nav 2 and Nav 3. You can probably take on the fighters at Nav 1. At Nav 2, however, switch to your camera pod and find the enemy fleet in the distance (no, you cannot catch up to them and you wouldn't want to even if you could; I've played the actual board game that this game is based on, and those capitol ships could destroy you faster than you can blink, especially in a light fighter like the Cheetah). Line up the fleet in the middle of your HUD, and hold down the trigger until the computer announces that your mission goals are complete. Let Mother keep the enemy off your back; that's what he's there for. After you get the data, you might have to turn back and finish off the enemy at Nav 2. As soon as you can, head for home and if you've taken ANY internal damage, do NOT engage the enemy. You can outrun them, and if the camera pod gets hit, you've lost the mission.
In the 3rd mission, just destroy as many enemies as you can before Mother gets hit and crashes. The mission automatically ends shortly after Mother gets hit, then you see the cinematic sequence. Now you're commander of the base.
From here on out, the missions are randomly generated. There are 3 levels of difficulty; you start day 2 at Medium difficulty. If you lose all three missions on day 2, then day 3 will be easier; if you win all three missions, day 3 will be harder. If you win at least one mission per day, you will stay on the Average path. Ultimately, your goal is to win on the Hard difficulty.
The game picks 9 wingmen randomly from a list of 20. The harder the difficulty you're on, the more likely it is that one of your wingmen will turn out to be a traitor. It can be any of your wingmen. Usually, you'll first realize there's a traitor when some of your other wingmen get poisoned or equipment gets sabotaged. You'll find the traitor sooner or later.
There are several types of missions: Surveillance, Strike, and Escort are the three most common. In a Strike mission, you're trying to rack up kills. Sometimes, if there's an enemy freighter along the way and you destroy it, you might capture one or two enemy fighters which you can then use.
In an Escort mission, you've got to protect an incoming freighter (or freighters). If you succeed, you'll usually get one or two new fighters.
In a Surveillance mission, YOU must carry the Surveillance Pod. You can put a Surveillance Pod on one of your wingmen's fighters, but they'll never use it. It's up to you to get the data. Remember, on a surveillance mission, that the goal is reconnaisance, not kills. If the camera pod gets destroyed, you've lost the mission.
Each mission has 4 nav points. At each nav point, the game randomly selects an encounter from a list of pregenerated encounters, based on whether you're on the Easy, Average, or Hard path, and the type of mission you're on.
If you want to cheat: Your saved game is actually a PLAIN TEXT file. There are 2 files with character data; one is for the previous mission (a backup file) and one is for the mission you just flew. The filename starts with the first eight letters of your character's name, not counting spaces. For example, if your character's name is Black Wolf, then the savegame will start with BLACKWOL.* (sorry, I forget the extension... it's been a while since I've played).
If you die and lose the game, just quit to DOS and copy the backup file over the current file. You'll go back one mission, but you get to continue the game.
If you edit these files, it'll be obvious which one is the current file and which is the backup; the current file will usually be longer by a few bytes. Plus, the day and mission number is recorded in the file. Some of the things you can edit: You can repair your ships, you can bring your dead wingmen back to life, you can force the game into Hard difficulty mode, and so on.
It is not recommended that you change one of your wingmen's names. If you change a name, make sure that it is one of the other pilots in the game, and it must be exactly spelled. Even the slightest mistake will cause the game to crash. The same applies to ship names.