ICftD is for the hardcore interactive sci-fi player. Mastering the various mini-games is necessary to completing it, though the most important ones are the side-scrolling parts and "Exterminator", where you shoot ants while they're trying to chew up a human tied to the ground.
Spoilers below:
Your ultimate mission is to find and eliminate the Antmind Queen, who lives three levels into the ground during the side-scrolling missions. In order to find her, you have to descend to the lowest point of the tunnels. There, you will run into her force field shield. Once you see the doctor after that, he will instruct you to obtain three transponders, which can be gained by engaging in and winning Exterminator three times. If you take too long in getting the transponders, you will run into Prissy, who has been overtaken by the Antmind. By this point in the game, Exterminator is almost impossible to win, and you will likely lose the codes to the force field. Since you won't have enough time to engage Exterminator three more times (and especially at the heightened difficulty level), you would only be able to get the first ending. However, if you're able to get to the force field after unlocking it, you will enter the final battle with the Antmind Queen. If you are hit while battling her (count on it happening more than once), entering the tunnels again will take you right back to her lair so you don't have to go through the tunnels all over again. Once you beat the Antmind Queen, you get the good ending. So, the key to winning is to first get to the lowest levels of the tunnels as quickly as possible to unlock the force field. Once you've broken into the Queen's lair, all subsequent entries into the tunnel give you another shot (haha, punny) at the good ending. I should also point out that many parts of the story are "useless" and serve no purpose. The important ones are saving Lud's place (free grenades for the rest of the game during the overhead battle scenes) and obtaining the Leaping Devastator (day 2, evening, saloon in Borax, choose Strength...allows you to jump FORWARD instead of backward while in the tunnels). You can also gain an Air Strike attack for the overhead scenes if you bring an ant leg to the doctor...it has limited use but every bit helps.