Gems are used to open doors found in various levels in Keens 4-6. To open a door, just carry the gem to an appropriate gem holder in the vicinity of the door. Keen knows all about the gems and will put them in the holder.
Commander Keen's weapon of choice in Keen 4-6. The gun fires a green blast of energy, stunning anything that happens to get in the way. You have a limited amount of shots so be sure to collect them if you happen to find one in a level. They are worth 5 ammo.