Quantum Theory is a fast-paced third-person shooter that introduces a dynamic cover system. When participating in intense firefights, you can use a variety of shooting techniques, from precise aiming to hip-firing or even blind shooting while behind cover. Each successful headshot is rewarded with a cinematic slow-motion image of the enemy's death, adding a visceral touch to combat.

Cid, the main character, has the unique ability to use Philena, his companion, as a throwing weapon, which further diversifies the combat strategy. In addition, Cid can seamlessly transition from using his weapons to delivering powerful melee attacks, sometimes triggering a devastating follow-up attack from Philena. Throughout the campaign, users face formidable bosses that require strategic identification of their weak points in order to succeed.

The action takes place in a post-apocalyptic world devastated by a devastating world war. The remnants of humanity have banded together into a resilient community known as Cocoon, whose lives are teetering on the brink due to the ruthless invasion of a malevolent force known as Erosion. This ominous black stuff changed the landscape, creating an otherworldly, organic sci-fi setting. United in the fight for survival, the people form a determined army to fight the relentless advance of Erosion.