The entire game is a simulation in a Zeerust future world.This would explain the Teleporter and the aliens.
The whole cave of Spelunky is a twisted gameshow or reality show.Contestants climb in for riches, contestants get chewed up by the deadly traps and criminals inside the cave, the viewers get to watch and enjoy. Anyone who survives is allowed to keep their money but has to return all the equipment and weapons they found... and they can dive into the cave for even more money if they desire.
"Kissing" the Damsels is just visual shorthand for something else.The Kissing Booths are lit by red lights, it costs upwards of $20,000 per "kiss", and it always (except for in the booths) takes place in completely safe "between" areas.
The City of Gold is a hallucination and you're just shoveling rocks and rubble into your pockets.The sheer psychological strain of getting the Hedjet and opening the sealed door, only to find nothing of value inside, loosens the Spelunker's grip on reality.
All the Damsels are actually men.Look at that face and try to tell me there's nothing definitively masculine about it.
Kissing the damsels is not a euphemism; that's actually all that goes on.The main hero is just so utterly terrible around women, that actually receiving any attention, let alone a kiss, significantly increases his will to live, more than any of the vast amounts of treasure he collects.
Each attempt is the Dying Dream of the previous Spelunker in a Mind Screwy reality warp perpetuated by dark, twisted magicks.When a Spelunker dies, their final moments are spent imagining a scenario where they made different decisions. If that adventurer fails, reality is warped just a little further as that explorer has their Dying Dream, and so on and so forth. The cycle is perpetuated by the restless spirits of all the hapless Virgin Sacrifices, Distressed Damsels and Adventurer Archaeologists trapped in this wretched, cursed land; if anyone actually makes it, their soul is free to move on, along with those of any they 'saved' during their successful journey. But for every fortunate soul that finally escapes the curse, countless more remain trapped in the cycle, making attempt after attempt...
The shotgun is an Evil WeaponThe shotgun is a cursed weapon. Notice how every shopkeeper sets up in a strange location and is willing to kill you over minor things. Notice that they also always have a shotgun. Coincidence? I think not. Finally, look at how many players murder the shopkeepers just to get it.
The skeletons are the remains of previous Spelunkers.Pretty much Exactly What It Says on the Tin. This explains, 1) why the Tunnel Man gets to keep his progress, even when your death is "undone", 2) why there are shops everywhere, including gambling parlors, and brothels. Still doesn't explain the crates, or why everything changes every time you come back, which leads to my next theory...
The game is the Spelunker equivalent of Valhalla.Instead of fighting and feasting for all eternity, the Spelunker gets to go on dangerous and glorious cave dives without worry of life or limb. It explains a lot of "inconsistencies", like the crates, the random dungeon, the shops, the Damsels who've survived apparently indefinitely without food or water... It's all part of our red-nosed protagonist's personal heaven.
The Spelunker is dead and the cave is HellThe spelunker died of dehydration in the desert. His spirit found the "cave," actually the portal to Hell, and he was compelled to enter due to his sin of greed. There he is forced to pass through the cave again and again, atoning for his sin. As for the rest of the game...
The Spelunker is a Favored Soul of Kali.Many people who play the game may eventually wonder why many parts of the cave only work for the Spelunker. Some traps will only trigger for him, enemies (with some exceptions) will only attack him and not other enemies, damsels, or shopkeepers, and for that matter, why is the Spelunker always blamed for the destruction of Kali's altars, even if he didn't do it? It's only explainable if he is in some way special. He is. He's a favored soul, sort of a "mini-avatar", a human who has been given slight amounts of his goddess' power and favor. He followed a trail of clues to the cave so that he could take Kali's test to see if he is worthy to gain her treasures.
Shops are found in the dungeon because they are illegalLet's start with the content of the shops: There are brothels, gambling parlors, and two distinct types of weapon store; one can possibly extrapolate that the specialty stores are in fact selling stolen military prototypes (explaining the jetpack) and so forth. In addition, the only collection of multiple shops in one level is called the Black Market, and yet contains nothing one would not find in a standard shop. This leads to the fact that all the shops are in fact illegal, and can only avoid being shut down by being set up in a treacherous dungeon.
The shopkeepers are Nazi war criminals.Given the nature of the spelunker as an Indiana Jones Expy one might notice the distinct lack of Nazis, prevalent in the Indian Jones series, but not to be seen here. Perhaps Spelunky takes place a decade or so after World War 2, and many Nazi officers fled to the cave to escape justice for their crimes. The higher technology such as the teleporter and the jetpack are easily explained: they're not inventions of an advanced humanity, but rather come from the aliens in area 3.
The lanterns in the stores are actually security cameras.That's how wanted posters with your picture are made,even when you kill the shopkeeper and you are the only one around.