There are three guns aboard your ship, which you choose from at the beginning of the game to defend yourself from whatever horrors await on the other side of the teleporter:
Each gun has four different primary and secondary firing modes, and you can change these by visiting upgrade robots.
Scattered throughout the game are various pickup guns. These have very limited ammunition, but give you a bit of flexibility. Picking up more than one of the same gun will add to its ammo count - you don't ever need to reload guns you find on the floor.
Occasionally, if you have a sharp eye, you might notice an orange bug skittering around. This little guy will disappear through a wall, and if you use a barrel to smash the wall down you will get to play with a secret gun.