Actually, I think the ending makes some sense. The player was infected- they got knocked down and were unconscious for a few hours, the notes stated that gasmasks weren't effective, and people who were infected end up as proxies under a degree of mind control, a mind control on the player that increases (and we hear him coughing repeatedly). The notes saying "Don't leave! Can't leave!"! was there to warn against fleeing the base- otherwise you'd be spreading the infection into the mainland. The bombs were there as an insurance plan that the fungus didn't escape- There was only one way out- you need a map, the snowcat, and gas, and so anyone in the facility who tried to leave would go for the map. The player was a dead man walking from the beginning.
