- Joystick: Use to direct the ship along the bottom of the screen. Push left to move the ship to the left, and right to move the ship to the right. Your ship can not pass beyond the side of the screen.
- Firing Button: Press the fire button to send one missile directly above your position. You can only send two missiles out at a time, but you have an unlimited supply of them.
- 1 or 2 Player Buttons: Push these buttons to begin a 1 or 2 player game.
This ship is under your control. You can move left or right, but you are relegated to the bottom of the screen. As in the previous Galaga game, your Fighter has a special ability to link up with other Fighters, allowing the two to work side by side, firing simultaneously. In order to accomplish this, you must allow one of your Fighters to be captured by a boss Galaga. At this point, your Fighter will turn red, and the next available Fighter will take its place. (Note that if you have no more available Fighters when you allow your current Fighter to be captured, the game will end.) In order to enable a double Fighter, you must rescue a red captured Fighter first.
Once you rescue a red captured Fighter, it will line up with your existing Fighter. At this point you can fire up to two missiles on to the screen at a time per ship. This means if you have two Fighters linked together, you can fire up to four missiles at a time. If you are struck by an enemy or a bullet, you will lose only one Fighter, while the other will remain. New to Galaga '88 is the potential for a double Fighter configuration to be captured by a boss Galaga. If this happens, the two Fighters will merge and create a blue captured Fighter.
If you manage to rescue a blue captured Fighter while in double formation, the blue ship will join your duo and create a triple Fighter, the most powerful formation available. A triple Fighter can shoot three bullets simultaneously, creating a wave of force that few enemies can escape. It is not possible to have your triple Fighter captured by a boss Galaga. If this formation is struck by an enemy or a bullet, it will revert back to a double Fighter formation.
There are two different kinds of capsules that can be collected throughout the game. The blue capsules can be collected in one of two ways. They are left behind by the obstacles that appear on most non-bonus stages when you destroy them, and they are generated by the enemies which are generated when two small enemies join together to make one bigger enemy. Collecting one will make your ship invincible for a very short period. Once you have collected two of them, they will create a dimensional rift after you have cleared the next bonus stage. Even after you reach the fifth and final dimension, it is still possible to collect them.
Pink capsules are left behind by the last enemies remaining on Stage 15 of Dimension 4, and Stage 25 of every Dimension if you manage to kill them before they escape. Collecting one will instantly transform your Fighter into a triple formation with no cost at all to your remaining lives. Both types of warp capsules are worth 500 extra points when collected, and will disappear forever if you miss them.
Like its predecessor, Galaga '88 has indicator badges to show what level you are currently on. A combination of these will add up to your current level. However, unlike its predecessor, there are only a limited number of stages to visit and the tally will stop at stage 29. One extra icon, the star on the right, is found in the game among the other badges, but does not correspond to any known stage.