Proton cannons are made of three pieces: a rectangular piece on the back, and two "L" shaped pieces on the block.
Proton cannons are placed on the walls of the level Blue is in, and they will periodically fire orange enzyme bullets. The proton cannons will fire the bullets straight, opening the "L" shaped pieces to fire the bullet.
Proton cannons, unlike mines, can be destroyed. To destroy the proton cannons, the hazard has to be struck three times with a proton bullet from Blue's own proton cannon. When proton cannons explode, they will not respawn. The orange enzyme bullets fired by the cannon will instantly kill Blue on contact. Also, the cannons are placed in many different locations in the levels.
Once the proton cannon fires a bullet, it will wait for the bullet to explode or hit a wall until firing again. A variation of the proton cannon, introduced later in Test Subject Blue, is the detection proton cannon, a more deadlier version of the proton cannon attached to the ceiling instead of walls, and being weaker than the usual proton cannons.
Proton cannons act the same as they did in Test Subject Blue, only in this game they take two blows to kill instead of three.
- Proton cannons are actually reverse-engineered versions of Blue's proton cannon that fire orange enzyme bullets instead of blue enzyme bullets.
- In Test Subject Blue, proton cannons can take three blows from Blue's proton cannon before exploding. In Test Subject Green, they can only take two blows.