In the Total War level, the Gas Mask is only available when someone brings the enemy canister to the central room of the tunnels. It is used to avoid the deadly toxic gas released by the canister. A gas mask can be attained from a normally sealed closet in the main area of either base. After using one, you will need to rearm with a weapon of choice.
In Conker's Bad Fur Day and Conker: Live and Reloaded, Conker has a gas mask with him, which he uses to avoid the stench while in Poo Mountain and the Poo Cabin. In Live And Reloaded, Conker's gas mask is changed to black instead of green.