The Eighth Doctor: Spore is about a "nightmare" pathogen that kills everything it touches, turning all life forms into black jelly and cobwebs, and the pathogen is on Earth, near Area 51 in Nevada. The Doctor doesn't have a companion, but he eventually makes contact with a woman who has survived the pathogen, and there's the question of whether or not she'll leave with him.
Killer diseases have been done to death in American literature, from The Andromeda Strain to The Stand, and this story does have some similarities with those popular novels; the military is called in, of course, but there the paths diverge. The Eighth Doctor arrives in his usual garb ("I was at the opera," he explains), takes charge, and immediately disappears into the infection, itself. The solution is kind of neat, and I liked the story. ****