The Soul Gems are six sacred gemstones which serve as the primary power source for the Beacon of Souls. Madame Leota's ghostly friends secured and hid five of the gems throughout the mansion to prevent them from falling into the hands of Atticus Thorn. One gem was still in place to allow the Beacon to function (albeit rather weakly). Zeke Holloway progressed through the mansion and acquired the remaining gems, one at a time.
- White: Fires standard shots, but also fires Rapid Shots.
- Purple: Power Shots which can take out stronger enemies.
- Orange: Ultra Shots which wipe out groups of enemies.
- Yellow: Upgraded Rapid Shots. Fires in three directions.
- Blue: Upgraded Power Shots. Affects enemy groups.
- Red: Upgraded Ultra Shots. Spreads damage between enemies.