The HoverCrate is a floating crate that can be used to store different things. The player picks the crate up by pressing the B button on the N64 controller or the A button on the Xbox 360 controller.
- Carrington Institute - On the main menu, when wandering around the Institute, one appears in the hangar.
- Area 51: Rescue - Jonathan gives a HoverCrate full of explosives to Joanna to use to blow a hole in a wall to access the lab area of the facility. If the crate is destroyed, the mission is failed, although it is possible to use the Dragon's secondary fire to blow up the wall.
- One appears in the Warehouse multiplayer level.
- If the player picks up and drops the crate repeatedly while moving, they can run faster than normal. This can help with speed runs.
- The player can use crates to hold doors open. The only real use for this is in the Carrington Institute menu area. If the player uses the crate to hold a door open in the Firing Range, they can use a fly-by-wire Slayer rocket to view areas outside the Institute and find the hidden Cheese. It is unknown if this was intended by the developers or not.