In keeping with the biomechanoid theme of the Alien Sphere, most of Prey's weapons are also hybrids of both mechanical and living parts.
Tommy's Pipe wrench, used as an improvised mêlée weapon. Holding primary fire swings it back and forth quickly, while holding secondary fire makes Tommy bring it above his head for a more powerful strike when released.
An automatic weapon which fires bolts of energy at a medium rate. Secondary fire causes an appendage to emerge from the weapon and attach itself to Tommy's eyeball, augmenting his vision with a zoomed-in "scope" view. The zoom can be further magnified too. In this mode, creatures glow brightly when the targeting area passes over them, making them highly visible. Also, while zoomed, the Rifle fires only single shots which are much more powerful and use more ammo.
Small, 3-legged crab-like creatures which are found roaming all over the Sphere. Can be used in two ways: by ripping off all of its legs and throwing the abdomen, it becomes like a grenade which explodes after a couple of seconds. Ripping off just one leg and throwing will make the crawler become like a proximity mine; attaching to whatever surface it lands on and exploding when a creature comes near. Pressing secondary fire makes Tommy flip the Crawler over to select which way to use it.
A powerful and versatile weapon. Ammo is gained by using the secondary fire to draw energy from nodes found throughout the Sphere. Different nodes make the gun take on different properties:
- Plasma (red glow): fires fast-moving balls of energy causing moderate damage;
- Freeze (light-blue glow): short-range attack which turns enemies into ice;
- Lightning (white sparks): fires a bolt of electricity — one or two shots kill most enemies, but "ammo" is more limited than with other types;
- Sunbeam (orange glow): a violently incandescent beam which cuts down most enemies almost instantly, as well as pushing the player back while firing.
A rapid-fire, multi-barrel machine gun complemented with a secondary fire which lobs grenade-like orbs from an orifice above the gun barrels, exploding on impact. Continuous use of the primary fire will make the gun overheat and stop firing for a moment until it cools down again.
Created by the friendly Hiders. A shotgun-style weapon which sprays acid rather than buckshot. The primary fire is deadly at close range, but much less effective at further distances. The secondary fire launches the entire vial of acid, which can be lethal if the shot hits its mark. Skillfully-aimed shots with the secondary fire can be rebounded against walls and around corners and so on.
A rocket propelled grenade-type weapon with Crawlers used as the ammo (although this is not shared with the individual Crawlers that are used as hand grenades). Primary fire shoots in a straight line to the target, exploding and causing damage in a large radius. Secondary fire vaporizes the Crawler into a lingering cloud of acid, effectively creating a shield in front of Tommy which dissolves any projectiles that come into contact with it.
Tommy's only weapon while spirit walking. Its ghostly arrows are powerful and effective over a long range, but with a relatively slow firing rate. At certain points in the game, it has some special uses which cannot be done with any other weapon.
Tommy's spirit guide, appearing in the form of a translucent blue hawk. In addition to guiding the player through the levels, perching on controls that need to be activated, and translating most of the alien speech and text visible on screens, Talon will also attack any nearby enemies (glowing red as he does so), providing a useful distraction. However, Talon can not be controlled by the player other than to make it follow.