At first this appears absurd, neither story line mentions the other, right? Well, that is almost correct. When viewed through a meta-world lens, a realization that there is more to every story and by gathering subtle clues and adding up minor details, we see that the worlds may be the same.
First there is a line from WH13 where Jane Latimer, Pete’s mother and a regent, and later The Guardian, mentions that (paraphrased to save time) Regents are advisors with specialized knowledge, the first agents, whose connection to the Warehouse must remain a secret.
Then there is The Last Crusade (TLC) and The Crystal Skull (CS), where we see a secret warehouse in the middle of nowhere, that looks kind of like the South Dakota badlands, that appears to have very few people manning it, though it is quite large, and Jones does have access…
Not so farfetched after all, hunh?
In TLC, taking place at the height of WWII, the Nazis are looking for relics of great power, normal people would either look at these relics, or artifacts as curios or just subjects of great narrative, Indiana Jones however knows that this is true, some things just cannot be explained with rational science.
Now this is before the internet, where one person could surf the web for days and find curiosities that should be investigated, so in order to find and collect artifacts there would need to be an extensive network in place, a network that probably includes archeologists that take random trips abroad finding powerful pieces like the Grail, the Ark, cool stones that let you pull a beating heart from a guy’s chest, a Crystal Skull… Not to mention, in the TV series, Young Indiana Jones, he is a very prolific figure across the globe.
So, we have a professor that knows artifacts have power, who was very adventurous and prolific, a secret to keep, a vast group of conspirators all looking to find artifacts, and an artifact that kills people that look inside it. At first it appears that Jones played little part in his own movie, as suggested by Amy Farrah Fowler in Big Bang Theory, but the meta-lens suggests he was, at this time a great puppet master.
As a regent, he knows that these things exist and that some people would use them for untoward ends, he also knows that given enough time the Nazis would find the Ark. If they did so on their own, it could be disastrous. He also knows that he can’t tell anyone about his connection to the Warehouse, and without the global information maven known as the internet, time is at a premium and the message could be compromised, the world is at war, and each power is vying for more power after all, we also know from CS, that he is a master manipulator: convincing the Russians to disarm themselves while they look for the container with the alien Skeleton (maybe he knew where it was the whole time?). So he sets out with a plan to lead the Nazis to the Ark by pretending to be trying to find it ahead of them, in essence leading them to the artifact, and perhaps manipulating them to take it to a secret location to release its power, destroying most of the occult believers of the SS and preventing others from wanting to follow in one fell swoop, at the end of which he turns it over for safekeeping at K29ZZZ (the Warehouse).
He may also have been an adviser for the Stargate program (before the SGC), in that series.