The Transition of Juan Romero

The Transition of Juan Romero takes place in a mining camp, presumably in Mexico as the deity Huitzilopochtli is mentioned.

While digging, a deep chasm is uncovered; "too deep for any sounding lines to hit bottom".  The night after the discovery of the abyss the narrator and one of the mine's workers, Juan Romero, venture inside the mine, following a mysterious rhythmical throbbing sound. Romero reaches the abyss first and is swallowed by it. The narrator peers over the edge, sees something - "but God, I dare not tell you what I saw!" and loses consciousness. The next morning Romero and the narrator are found in their beds; Romero dead. The other miners swear that no-one left the bunk house...

Huitzilopochtli is a deity dedicated to war, sun and human sacrifice; quite why he's linked to a deep chasm and people dying in their sleep is a bit weird... but this is Mythos we're talking about here. As a deity, he can be transferred to a number of different situations, many of which would be far more suitable. I would imagine sacrifices at sunrise and sunset would be more appropriate.

In terms of converting this to a WW2 mission there's not a lot in the overall plot that ties it to a specific time period, so maybe the investigators have been sent to investigate a series of mysterious deaths a mine. If they only visit during the day they probably won't find much, but if they stay overnight, you could start to introduce elements of the Dreamlands into the meta plot. Normally dying in the Dreamlands would return you to your sleeping form, but occasionally the shock of seeing through the breach and realising that it's real could cause complete heart failure, especially if something hideous like an Elder God, or the city of Leng are seen.

Huitzilopochtlimay be local superstition that is being blamed for the deaths, or he may actually be a facet of an Elder God...

The Sonman Mine Explosion

Literature isn't the only source of weird and wonderful events that could act as plot points.

In 1940, the Sonman Mine near Portage, Pennsylvania was the site of a large explosion that killed an estimated 63 miners. Rescue was severely hampered by a methane gas buildup that filled the tunnels, especially around the area called Right No. 16 heading where the explosion is said to have been centered.

While this can easily be explained as a gas explosion, it could also be a coverup for something far more sinister.

Mines can be a good source of mythos related investigations as you never quite know what could have been in those tunnels. In this case there are a few likely variants on this tale

1) The investigators are called in after the explosion to investigate some odd findings in the mining company's rescue attempts; possibly some body parts that couldn't possibly belong to any of the workers, or part of a strange carving.

2) The more fun one is to have the investigators called in to look at something uncovered in the tunnels during the mining. This could be something as simple as an odd mineral or some cave markings in a sealed cave; all the way up to carved tunnels uncovered during the excavation. To explain the disaster, you're likely going to want to have something really nasty hiding in there that needs lots of explosives to stop it escaping.

Markham Colliery Disaster

Markham Colliery at Staveley near Chesterfield, Derbyshire, England suffered a massive explosion on the 10th of May, 1938 that killed 79 miners. It is believed that the explosion was caused by a runaway truck that cut an electric cable and released coal dust into the air; this combination would have been lethal.

The Markham No. 1 Colliery is situated about four miles east of Chesterfield. Mining work began at this site about 1882, but the Blackshale Seam, where the explosion was centred, was not reached until 1924 or 1925. No coal mining was taking place in this part of the mine in 1938; it is believed that the truck collided with containers full of  waste material accrued during the cleaning of the gearheads and loader gates.

Lots of information about the real event on: http://www.healeyhero.co.uk/rescue/pits/markham/markham_38.htm#top

It all sounds far too neat. I suspect the miners dug through into a nest full of Ghasts and causing the explosion was the only way to stop them from escaping